Biological Information

Key concepts:
• DNA is the primary macromolecule used to store biological information.
• a gene is a length of DNA that codes for a single polypeptide chain.
• during transcription a copy is made of a gene, or genes, worth of information. This copy is in the form of RNA and is called messenger RNA or mRNA.
• in eukaryotic cells (such as human or plant cells) the mRNA is processed and modified in various ways. Un-needed or extra information is removed.
• the mRNA moves to the cytoplasm where the "decoding" of the instructions takes place.
• during translation the genetic code in interpreted and the amino acids are joined together in the correct sequence as specified by the gene.
• the polypeptide so formed folds up into a functioning protein.
• the protein performs some task (catalyzing a reaction, in the case of an enzyme).
• the trait is seen (red flowers, in this case).

The Genetic Code

Key concepts:
• the genetic code has an alphabet of four letters A, T, G, and C. These are the nucleotide bases Adenine, Thymine, Guanine and Cytosine.
• the genetic code, however, is most usually written using the nucleotide bases found on the mRNA molecule. These are A, U, G, and C.
• the "letters" of the alphabet are grouped into "words" of three letters each. On the mRNA molecule each "word" of three letters is called a codon.
• a single codon specifies, or "codes for", a single amino acid.
• there are 64 codons, but only 20 common amino acids. Many amino acids, therefore are coded for by more than one codon. The genetic code is said to be redundant.
• codons are arranged in a linear sequence along the DNA gene (and the mRNA transcript) with no gaps and no overlapping between words.
• the sequence of codons specifies the order and sequence of amino acids on the final polypeptide chain.

Ribosomes

Key concepts:
• ribosomes are complexes of RNA (special RNA transcripts called rRNA) and proteins.
• an intact bacterial ribosome, called a 70S ribosome, is made up of two subunits, a large subunit (50S) and a small subunit (30S).
• the large subunit contains 31 proteins a 23S molecule of rRNA and a 5S molecule of rRNA.
• the small subunit contains 21 proteins and a molecule of 16S rRNA.
• when not active in protein synthesis, the ribosomes separate into subunits in the cytoplasm of the cell.

Transfer RNA

Key concepts:
• tRNA molecules are an average of 76 nucleotides in length and contain many highly modified bases.
• tRNAs have a secondary structure in which regions of the molecule base pair to form a "cloverleaf", with a "stem" and three main loops.
• a single amino acid is joined to the very end of the "stem" region by an enzyme. ATP is used as a source of energy.
• the "loop" of RNA opposite the "stem" bends in such a way that three nucleotide bases stick out. These three bases are called the anticodon.
• special enzymes are used to join amino acids to tRNAs. The specificity of these enzymes ensures that a specific amino acid is joined to a specific tRNA in a unique arrangement. These is one specific tRNA for each amino acid.

Translation: Getting started

Key concepts:
• in bacterial mRNA the process begins when the small ribosomal subunit binds to the mRNA.
• a nucleotide sequence on the mRNA situated just before the first codon base pairs with a complementary sequence on the 16S ribosomal RNA of the small ribosome subunit.
• the full ribosome forms as a large ribosomal subunit joins with the small ribosomal subunit and the mRNA.
• also involved is a special type of tRNA (with its amino acid) called initiator tRNA
• help is also needed from three initiation factors and energy in the form of GTP.
• once assembled the ribosome has two regions on its surface where tRNA molecules can bind, these are the A- and P- sites.
• these sites for tRNA binding are in a cleft of the small ribosomal subunit, where all the action of decoding the mRNA takes place.
• the initiator tRNA and its amino acid (modified methionine) sits in the P-site with its anticodon base pairing with the initiation or start codon on the mRNA molecule.

Translation: Elongating the polypeptide

Key concepts:
• a tRNA molecule with its amino acid is delivered to the A-site on the ribosome.
• the anticodon on this tRNA must be an exact complementary match for the next codon on the mRNA molecule.
• the ribosome now has both sites (the A- and the P-sites) occupied with tRNA molecules and their amino acids.
• a protein that is part of the large ribosomal subunit removes the amino acid from the tRNA in the P-site and transfers it over to the amino acid that is currently in the A-site.
• a peptide bond is formed between these two amino acids.
• a complex of protein and GTP binds to the ribosome and several things happen all at once.
• the tRNA without an amino acid is ejected from the P-site.
• the tRNA with the peptide is now moved over from the A-site to the P-site.
• the mRNA moves by one codon's worth of information. The initiation or start codon leaves the ribosome and the next codon is brought into alignment with the empty A-site.
• the elongation cycle is now complete and can begin all over again

Translation: The end

Key concepts:
• the stop codons are UAA, UAG and UGA.
• the is no tRNA molecule with an anticodon that matches any of these stop codons.
• when the ribosome reaches one of these stop codons on the mRNA a release factor recognizes the codon and makes the protein on the large ribosomal subunit transfer the polypeptide to a water molecule, not another amino acid.
• this causes the release of the completed polypeptide from the complex.

Completing the Protein

Key concepts:
• correct folding of the polypeptide begins with the formation of regions of secondary structure (random walk, alpha-helix or beta-pleated sheet).
• tertiary structure is the result of the giant molecule folding further to minimize the exposure of hydrophobic amino acids to the water and maximize the exposure of hydrophilic amino acids.
• sometimes covalent bonds form between sulfur containing amino acids, further stabilizing the molecule.
• some proteins are reduced in size by enzymes that remove unwanted regions.
• some proteins are modified by the addition of extra material such as phosphate groups, methyl groups, sugars or even nucleotides.
• the final protein with all its amino acids in the right order (primary structure), folded (secondary and tertiary structure) and modified (quaternary structure), is now ready for action.

Mutations

Key concepts:
• the simplest mutations are those that alter or change a single base in the DNA sequence. These are called point mutations.
• two adjacent bases may be fused to one another. This is called a dimer.
• information may be removed from the DNA or gene. This is a deletion. Deletions may be small (a single base) or very extensive. The latter is usually fatal.
• information may be added to a DNA molecule. This is an addition. Once again, the addition may be as small as a single base, or as extensive as a whole block of genes.
• single base additions or deletions alter the way in which codons are read by the translation machinery by moving the reading frame by one base. These are called frame shift mutations.

Mutageneis

Key concepts:
• if a DNA molecule is struck by high-energy radiation, such as X-rays or gamma-rays, electrons are ejected from the molecule and thus cause extensive damage. Sometimes the DNA molecules break.
• lower energy radiation, such as ultra violet radiation, UV, causes adjacent thymidine bases to fuse together into a dimer.
• many different types of chemicals act and react in deleterious ways with the bases in a DNA molecule. Some cause direct mutagenesis by altering the base pairing, others alter the DNA and its properties.
• as cells try to repair this damage they make further mistakes which ultimately lead to permanently altered base sequences and thus permanent mutations. This sequence of events is called indirect mutagenesis.