Proteins

• An organism's genome is its complete set of DNA, although not all of this DNA codes for proteins.
• The proteome is the entire set of proteins that can be expressed by an organism's genome, and is much larger than the number of genes
• Alternative RNA splicing allows different proteins to be produced from the same gene.
• Alternative RNA splicing means that different combinations of coding regions called exons can be left in or removed during transcription to produce different mature MRNA transcripts, allowing different proteins with different structures and functions to be produced.
• Not all genes in the genome code for proteins, these are called non-coding RNA genes. Non-coding RNA genes can produce tRNA, rRNA and RNA molecules.
• There are various other factors that can affect protein expression, such as the metabolic activity of the cell, cellular stress, response to signalling molecules, and diseased vs healthy cells.
• Plasma membranes control what substances enter or exit a cell.
• Eukaryotes are cells with a true membrane bound nucleus.
• Eukaryotes also have a system of intracellular membranes which help with protein synthesis and transport in the cell.
• Structures that have intracellular membranes include the endoplasmic reticulum, the golgi apparatus, vesicles and lysosomes.
• The endoplasmic reticulum is a series of membrane tubules that extend from the nuclear membrane.
• Rough endoplasmic reticulum has ribosomes dotted along its surface whereas smooth endoplasmic reticulum does not.
• The Golgi apparatus is a series of flattened membrane disks that proteins can pass through to be modified.
• Transport vesicles carry proteins to the golgi apparatus and after the proteins have been modified they are released from the Golgi in secretory vesicles.
• Lysosomes are membrane bound organelles that contain hydrolases which are enzymes.
• Hydrolases use water to break the covalent bonds in proteins, lipids, nucleic acids and carbohydrates, and break them down.
• The main components of the plasma membrane are lipids and proteins which can both be synthesised within the cell at the endoplasmic reticulum.
• Lipids are synthesised in the smooth endoplasmic reticulum and are inserted into the smooth endoplasmic reticulum membrane.
• All protein synthesis within a cell begins at a cytosolic ribosome.
• Cytosolic ribosomes are found within the cytosol.
• Cytosolic proteins are synthesised at a cytosolic ribosome, and remain in the cytosol.
• Transmembrane proteins contain a signal sequence, which is a sequence of amino acids determining the location of the protein within the cell.
• In transmembrane proteins, the signal sequence halts translation, and directs the ribosome synthesising the protein to dock with the endoplasmic reticulum, forming rough endoplasmic reticulum.
• After a cytosolic ribosome docks with the endoplasmic reticulum, translation continues, and the protein is inserted into the endoplasmic reticulum membrane.
• Once proteins are in the ER membrane, they are transported by transport vesicles to the Golgi apparatus.
• As proteins move through the Golgi apparatus, they undergo post translational modification.
• Once post translational modification is complete, proteins are carried by secretory vesicles to the plasma membrane and lysosomes.
• One post-translational modification is the addition of carbohydrate groups, to form a glycoprotein. Enzymes catalyse the addition of sugars to form the carbohydrate.
• Proteolytic cleavage is another post translational modification where some of the peptide bonds within the protein are broken. This happens in some digestive enzymes to activate them.
• Protein polymers are formed from amino acid monomers, which are folded into shapes to determine the protein's function.
• Acidic R groups are hydrophilic, carry a negative charge, and the key component is a carboxylic acid group (COOH)
• Basic R groups are hydrophilic, have a positive charge, and their key component is an amine group (NH2)
• Polar R groups are hydrophilic, neutral, and their key components are carbonyl (CO) hydroxyl (OH) amine (NH2) or sulphdyl (SH) groups.
• Non polar r groups are hydrophobic, have no charge, and their key components are hydrocarbon groups.
• The primary structure of proteins is the unfolded chain of amino acids.
• The secondary structure of proteins is caused by hydrogen bond formation along the peptide backbone, and include: alpha helixes, beta pleated sheets and turns.
• The tertiary structure of protein folding is the overall shape of a folded protein, stabilised by R group interactions, including hydrophobic, London dispersal forces, ionic bonds, disulphide bridges and hydrogen bonds.
• Hydrophobic R group interactions are found where hydrocarbon groups come close together.
• London dispersal R group interactions are found when hydrocarbon groups come close together.
• Ionic bond R group interactions are caused by the electrostatic attraction between oppositely charged ions, and are often broken by changing pH.