2. proteins

• the genome is all of the hereditary information encoded in DNA
• 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
• the set of proteins expressed by a given cell type can vary over time and under different conditions
• the factors affecting the set of proteins expressed by a given cell type are:

  • metabolic activity of the cell
  • cellular stress
  • response to signalling molecules
  • diseased VS healthy cells
• not all genes are expressed as proteins in a particular cell type
• genes that do not code for proteins are called non-coding RNA genes and include those which are transcribed to produce tRNA, rRNA and RNA molecules that control the expression of other genes
• eukaryotic cells have a relatively small surface area to volume ratio, duo to their relatively large size
• the surface area of the plasma membrane on the eukaryotic cells is too small to carry out all the vital functions that rely on membranes and the specialised proteins associated with them
• to the increase the total membrane area, eukaryotic cells have a system of internal membranes, which are called the endoplasmic reticulum (ER)
• the endoplasmic reticulum forms a network of membrane tubules continuous with the nuclear membrane
• the endoplasmic reticulum can either be rough (RER) or smooth (SER)
• rough ER has docked ribosomes on its cytosolic face while smooth ER lacks these ribosomes
• the golgi apparatus is a series of flattened membrane disks which are connected and have associated vesicles that transport materials between membrane compartments
• the connected disks allow molecules to move within the golgi apparatus
• lysosomes and membrane-bound organelles which contain a variety of hydrolases that can digest:

  • proteins
  • lipids
  • nucleic acid
  • carbohydrates
• the interior of the lysosomes are acidic, allowing for optimal function of the enzymes it contains
• vesicles transports materials between membrane compartments, they consist of an aqueous solution enclosed by a lipid bilayer
• phospholipids and proteins are the main components of a cell membrane
• phospholipid molecules have a hydrophilic head and hydrophobic tail
• both lipids and proteins are synthesises in the ER
• lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane
• the synthesis of proteins begins in the cytosolic ribosomes
• the synthesis of the cytosolic proteins is completed at the cytosolic ribosomes and the proteins remain in the cytosol (cytoplasm) where they carry out specific functions
• the transmembrane proteins begin to synthesis in the cytosolic ribosomes, but is completed when the relevant cytosolic ribosomes dock with the ER to become part of the RER
• transmembrane proteins carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming the RER
• the signal sequence is a short stretch of amino acids at one end of the polypeptide that determines the eventual location of the protein in a cell
• Translation continues after docking, and the protein is inserted into the membrane of the ER
• Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus
• As proteins move through the Golgi apparatus they undergo post-translational modification
• post-translational modification refers to the covalent modifications which are made to proteins after translation
• The addition of carbohydrate groups is the major modification

  enzymes catalyse the addition of various sugars in multiple steps to form carbohydrates and glycoproteins are produced
• Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes
• Vesicles move along microtubules to other membranes and fuse with them within the cell
• secreted proteins are translated in ribosomes on the RER and enter its lumen
• peptide hormones (insulin) and digestive enzymes (trypsin) are examples of secreted proteins
• The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
• These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell
• Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins
• proteolytic cleavage is another type of post-translational modification