2. Proteomics, protein structure, binding and conformational change Flashcards
What is the proteome?
- 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.
How are genes expressed in a cell?
- Not all genes are expressed as proteins in a particular cell type.
- The set of proteins expressed by a given cell type can vary over time and under different conditions.
How are membranes structured in eukaryotes?
Eukaryotic cells have a system of internal membranes, which increases the total area of membrane.
What is the endoplasmic reticulum?
- The ER forms a network of membrane tubules continuous with the nuclear membrane.
- Rough ER has ribosomes on its cytosolic face while smooth ER lacks ribosomes.
What is the Golgi apparatus?
- The Golgi apparatus is a series of flattened membrane discs.
- The discs are connected allowing molecules to move within the Golgi apparatus.
- The Golgi apparatus is adjacent to the endoplasmic reticulum.
What are lysosomes?
Lysosomes are membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates.
What are vesicles?
- Vesicles transport materials between membrane compartments.
- They consist of an aqueous solution enclosed by a lipid bilayer.
Where are lipids and proteins synthesised?
- Lipids and proteins are synthesised in the ER.
- Lipids are synthesised in the 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.
What are transmembrane proteins?
- Transmembrane proteins carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER
- Translation continues after docking, and the protein is inserted into the membrane of the ER.
Describe movement of proteins between membranes
- Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus.
- Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack, as they move post-translational modifications take place.
- The addition of carbohydrate groups is the major post-translational modification.
What is the role of vesicles in the movement of proteins?
- 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.
Describe the secretory pathway.
- Secreted proteins are translated in ribosomes on the RER and enter its lumen
- 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
What are proteins?
- Proteins are polymers of amino acid monomers.
- A monomer is a molecule that may bind chemically to other molecules to form a polymer.
What is the structure of amino acids?
- Amino acids are linked by peptide bonds to form polypeptides.
- Amino acids have the same basic structure, differing only in the R group present.
- The wide range of functions carried out by proteins results from the diversity of R groups.
How are amino acids classified?
Amino acids are classified according to their R groups:
* basic (positively charged) - hydrophylllic
* acidic (negatively charged) - hydrophyllic
* polar - hydrophyllic
* hydrophobic - non-polar
What is primary structure?
The primary structure is the sequence in which the amino acids are synthesised into the polypeptide.
What is secondary structure?
- Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure
- These regions are either alpha helices, parallel or anti-parallel beta-pleated sheets, or turns.
- beta-sheets are parallel or antiparallel depending on their N and C termini.
What is tertiary structure?
- 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 bridge
What is quaternary structure?
- Quaternary structure exists in proteins with two or more connected polypeptide subunits.
- Quaternary structure describes the spatial arrangement of the subunits.
What is a prosthetic group?
A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.
How do pH and temperature affect proteins?
- Interactions of the R groups can be influenced by pH and temperature.
- This is why pH and temperature will affect the structure (and function) of a protein.
- Increasing temperature disrupts the interactions that hold the protein in shape
- As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost,
Describe ligand binding.
- A ligand is a substance that can bind to a protein
- R groups not involved in protein folding can allow binding to ligands
- Binding sites will have complementary shape and chemistry to the ligand
- As a ligand binds to a protein-binding site the conformation of the protein changes
- This change in conformation causes a functional change in the protein
What are allosteric interactions?
- Allosteric interactions occur between spatially distinct sites.
- Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits
- Allosteric enzymes contain a second type of site, called an allosteric site
- Modulators regulate the activity of the enzyme when they bind to the allosteric site
- Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
How does binding in haemoglobin demostrate cooperativity?
- Haemoglobin demonstrates quaternary structure in that is made up of four polypeptide subunits, each of which contain a haem group capable of binding a molecule of oxygen.
- When one of the subunits binds a molecule of oxygen, the second binds more easily, and the third and fourth easier still.
- This process is known as cooperativity; the ligand binding to one subunit of the protein has increased the other subunits’ affinity for the ligand.
How do temperature and pH affect haemoglobin’s ability to bind to oxygen?
- As temperature increases, affinity for oxygen decreases
- As pH decreases, affinity for oxygen decreases.
How are phosphates used in post-translational modification?
- Phosphorylation of proteins is a form of post-translational modification.
- The addition or removal of phosphate from particular R groups can be used to cause reversible conformational changes in proteins which can affect a protein’s activity.
What is the role of kinase proteins in phosphorylation?
- Protein kinases catalyse the transfer of a phosphate group to other proteins.
- The terminal phosphate of ATP is transferred to specific R groups creating ADP as well as a phosphorylated protein.
- Protein phosphatases catalyse the reverse reaction.
How does phosphorylation affect protein activity?
- Phosphorylation brings about conformational changes, which can affect a protein’s activity.
- The activity of many cellular proteins, such as enzymes and receptors is regulated in this way.
- Some proteins are activated by phosphorylation while others are inhibited.
