1.2 Proteomics

• The proteome is the entire set of proteins expressed by a genome
• The proteome is larger than the number of genes, particularly in eukaryotes, because more than one protein can be produced from a single gene as a result of alternative RNA splicing
• Genes that do not code for proteins are called non-coding RNA genes and include those that are transcribed to produce tRNA, rRNA, and RNA molecules that control the expression of other genes.
• Some factors affecting the set of proteins expressed by a given cell type are the metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells.
• Eukaryotic cells have a system of internal membranes, which increases the total area of membrane. Because of their size, eukaryotes have a relatively small surface area to volume ratio. The plasma membrane of eukaryotic cells is therefore too small an area to carry out all the vital functions carried out by membranes.
• The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane
• The Golgi apparatus is a series of flattened membrane discs
• Lysosomes are membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates
• Vesicles transport materials between membrane compartments
• Rough ER (RER) has ribosomes on its cytosolic face while smooth ER (SER) lacks ribosomes.
• Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane
• The synthesis of all proteins begins in cytosolic ribosomes The synthesis of cytosolic proteins is completed there, and these proteins remain in the cytosol
• A signal sequence is a short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.
• 1.Transmembrane proteins carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER.
• 2.Translation continues after docking, and the protein is inserted into the membrane of the ER
• 3. Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus
• 4. As proteins move through the Golgi apparatus they undergo post-translational modification. Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack. Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates
• The addition of carbohydrate groups is the major modification
• 5. Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes
• 6. Vesicles move along microtubules to other membranes and fuse with them within the cell
• 1. (sp) Secreted proteins are translated in ribosomes on the RER and enter its lumen
• Peptide hormones and digestive enzymes are examples of secreted proteins.
• 2. (sp) The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
• 3. (sp) These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell
• 4. (sp) Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins
• Proteolytic cleavage is another type of posttranslational modification. Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.
• Amino acid sequence determines protein structure.

  Proteins are polymers of amino acid monomers
• Amino acids are linked by peptide bonds to form polypeptides
• Amino acids have the same basic structure, differing only in the R group present.

  R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity.
• Amino acids are classified according to their R groups:

  basic (positively charged)

  acidic (negatively charged)

  polar

  hydrophobic
• The primary structure is the sequence in which the amino acids are synthesised into the polypeptide
• Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure — alpha helices, parallel or antiparallel beta-pleated sheets, or turns
• The polypeptide folds into a tertiary structure

  This conformation is stabilised by interactions between R groups: hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges
• Disulfide bridges are covalent bonds between R groups containing sulfur.
• Quaternary structure exists in proteins with two or more connected polypeptide subunits
• Quaternary structure describes the spatial arrangement of the subunits.
• A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function
• The ability of haemoglobin to bind oxygen is dependent upon the non-protein haem group.
• Interactions of the R groups can be influenced by temperature and pH

  Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured. The charges on acidic and basic R groups are affected by pH. As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.
• A ligand is a substance that can bind to a protein