Biochemistry

• Amino acids are joined together by peptide bonds, which involve the formation of a molecule of water in another condensation polymerisation reaction.
• When two amino acids join together, a dipeptide is formed.
• Three amino acids form a tripeptide.
• Many amino acids form a polypeptide.
• In a polypeptide, there is always one end with a free amino (NH2) group, called the N-terminus, and one end with a free carboxyl (COOH) group, called the C-terminus.
• A protein is a polypeptide chain many hundreds of amino acids long.
• Amino acid polymerisation to form polypeptides is part of protein synthesis, which takes place in ribosomes and requires an RNA template.
• The sequence of amino acids in a polypeptide chain is determined by the sequence of the bases in DNA.
• Polypeptides are just strings of amino acids, but they fold up and combine to form the complex and well-defined three-dimensional structure of working proteins.
• The primary structure of a protein is just the sequence of amino acids in the polypeptide chain, which determines the rest of the protein structure.
• The secondary structure of a protein consists of a few basic motifs that are found in almost all proteins, held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone.
• The tertiary structure of a protein is the complete structure formed by the folding up of a polypeptide chain, which is responsible for its properties and function.
• The tertiary structure of a protein is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is.
• These bonds include hydrogen bonds, which are weak but numerous, and ionic bonds (or salt bridges) between oppositely-charged R-groups such as NH3+ in lysine or arginine with  COO in aspartate or glutamate.
• Hydrogen bonds are weak and can break and form spontaneously at the temperatures found in living cells without needing enzymes.
• Water is essential for life on Earth as all living organisms depend on water.
• At least 80% of the total mass of living organisms is water.
• Water molecules are a charged dipole, with the oxygen atom being slightly negative ( -) and the hydrogen atoms being slightly positive ( +).
• The dipole property of water gives it many specific properties that have important implications in biology.
• Water is an extremely good solvent and the water dipoles will stick to the atoms in almost all crystalline solids, causing them to dissolve.
• Many important biological molecules ionise when they dissolve, so the names of the acid and ionised forms (acetic acid and acetate in this example) are often used loosely and interchangeably, which can cause confusion.
• Water has a high specific heat capacity, which means that it takes a lot of energy to heat, so water does not change temperature very easily.
• Water requires a lot of energy to change state from a liquid into a gas, since so many hydrogen bonds have to be broken, so as water evaporates it extracts heat from around it, and this is used to cool animals (sweating and panting) and plants (transpiration).
• Water is cohesive and adhesive, explaining why long columns of water can be sucked up tall trees by transpiration without breaking and why water molecules stick to other surfaces, such as xylem vessels.
• Water is most dense at 4°C, causing several important effects: ice floats on water, so as the air temperature cools, bodies of water freeze from the surface, forming a layer of ice with liquid water underneath.
• The expansion of water as it freezes causes freeze-thaw erosion of rocks, which results in the formation of soil, without which there could be no terrestrial plant life.
• The anticodon of tRNA attaches to the first mRNA codon by complementary base pairing.
• The next amino acid-tRNA attaches to the adjacent mRNA codon (CUG, leu in this case) by complementary base pairing.
• The bond between the amino acid and the tRNA is cut and a peptide bond is formed between the two amino acids.
• These operations are catalysed by enzymes in the ribosome called ribozymes.
• The ribosome moves along one codon so that a new amino acid-tRNA can attach.
• The free tRNA molecule leaves to collect another amino acid.
• The cycle repeats from step 3.
• The polypeptide chain elongates one amino acid at a time, and peels away from the ribosome, folding up into a protein as it goes.
• This continues for hundreds of amino acids until a stop codon is reached, when the ribosome falls apart, releasing the finished protein.
• 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 polyribosome, or a polysome.
• In eukaryotes, proteins often need to be altered before they become fully functional, a process called post-translational modification.
• Modifications are carried out by other enzymes and include chain cutting, adding methyl or phosphate groups to amino acids, adding sugars (to make glycoproteins) or lipids (to make lipoproteins).
• A mutation is a change in DNA in a cell (a change in genotype) and it may have no effect on phenotype or it may have a major effect, including death.