Proteins Flashcards
The proteome
The entire set of proteins expressed by a genome
Why is the proteome larger than the number of genes?
More than one protein can be produced from a single gene as a result of alternative RNA splicing
What are genes that don’t code for proteins called?
Non-coding RNA genes, they include those transcribed to produce tRNA, rRNA and RNA molecules that control expression of other genes.
What are some factors affecting the set of proteins expressed by a given cell type?
The metabolic activity of the cell, cellular stress,the response to signalling molecules and diseased vs healthy cells.
The endoplasmic reticulum (ER)
Forms a network of membrane tubules continuous with the nuclear membrane.
The Golgi apparatus
A series of flattened membrane discs.
Lysosomes
Membrane - bound organelles containing a variety of hydrolyses that digest proteins, lipids, nucleic acids and carbohydrates.
Vesicles
Transport materials between membrane compartments.
Where are lipids synthesised?
In the smooth endoplasmic reticulum and inserted into its membrane.
Where does the synthesis of all proteins begin?
The cytosolic ribosomes
Signal sequence
A short stretch of amino acids at are end often polypeptidethat determines the eventual location of a protein in a cell.
Transmembrane protein synthesis
Begins in cytosolic ribosome, a signal sequence halts translation and directs the ribosome synthesising the protein to duck with the ER, forming RER. Translation continues after docking, and the protein is inserted into the membrane of the ER
What happens to proteins once they are in the ER?
They ere transported by vesicles that bud off from the ER and fuse with the Golgi apparatus.
How do molecules move through the Golgi apparatus?
In vesicles that bud off from are disc and fuse to the next one in the stack
How are carbohydrates formed in the Golgi apparatus?
Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates.
What is the major modification in the Golgi apparatus?
The addition of carbohydrate groups
What are the fates of proteins that leave the Golgi apparatus?
Vesicles take proteins to the plasma membrane and lysosomes.
How do vesicles move?
Vesicles more along microtubules to other membranes and fuse with them within the cell.
How are secreted proteins produced?
Translated in ribosomes on the RER and enter its lumen. The proteins move through the Golgi apparatus and are then packaged into secretary 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 end require proteolytic cleavage to produce active proteins.
Examples of secreted proteins.
Peptide hormones and digestive enzymes.
What is proteolytic cleavage?
Another type of post-translational modification,
A secreted protein that requires proteolytic cleavage to became active?
Digestive enzymes,
What determines protein structure?
Amino acid sequence
What are proteins?
Polymers of amino acid monomers
How do r groups of amino acids vary?
Size, shape,charge, hydrogen bonding capacity,chemical reactivity
What are the classification of amino acids?
Basic ( positively charged), acidic (negatively charged), polar and hydrophobic
Primary structure
The sequence in which the amino acids are synthesised into the polypeptide.
Secondary structure
Hydrogen baking along the backbone of the protein strand results in regions of secondary structure - alpha helices, parallel or anti-parallel beta-pleated sheets, or turns.
Tertiary structure
The polypeptide folds into tertiary structure, this conformation is stabilised by interactions between r groups.
What interactions between r groups are involved in tertiary structures
Hydrophobic interactions, ionic bands,London dispersion forces, hydrogen bonds and disulphide bridges
Quaternary structure
Describes the spatial arrangement of the subunits.it exists in proteins with two or more connected polypeptide subunits.
Prosthetic group
A non-protein unit tightly boundto a protein and necessary for its function
Example of prosthetic group
The ability of haemoglobin to bind to oxygen is dependant upon the non-protein haem group.
How does increasing temperature influence interactions between r groups
Increasing temperature disrupts the interactions holding the protein in shape, the protein begins to unfold eventually becoming denatured.
How does changes in pH affect interactions between r groups?
The charges an acidic and basic r groups are affected by pH. As pH moves away from the optimum, the normal ionic interactions between charged groups a lost, which gradually changes the conformation of the protech until it becomes denatured.
Ligand
A substance that can bind to a protein
What allows binding of legends?
R groups not involved in folding of the protein
How do binding sites bind to ligands?
They will have complementary shape and chemistry to the ligand
What happens to a protein when a ligand binds?
The conformation of the protein changes. This change in conformation causes a functional change in the protein
Where do allosteric interactions occur?
Between spatially distinct sites.
What happens to the affinity of on allosteric site after a substrate binds and why is this biologically important?
The binding of a substrate molecule to are active site of an allosteric enzyme increases the affinity of the other active sites for banding of subsequent substrate molecules. This is of biological importance because the activity of allosteric enzymes con vary greatly with small changes in substrate concentration.
What is co-operativity in binding?
Changes in binding at ae subunit alter the affinity of the remaining subunits
What kind of things have co-operative binding?
Allosteric proteins with multiple subunits.
Allosteric site
A second type of site en a allosteric enzyme
Modulates
Regulate the activity of the enzyme when try bind to the allosteric site
How does a modulator work?
Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
Positive modulators
Increase the enzyme’s affinity for the substrate
Negative modulators
Reduce the enzyme’s affinity for the substrate
Example of co-operativity
The binding and release of oxygen in haemoglobin. Changes in binding of oxygen alone subunit after the affinity of the remaining subunits for oxygen.
The influence and biological importance of temperature and pH on the binding of oxygen.
A decrease in pH or an increase in temperature lowers the affinity of haemoglobinfor oxygen, so the binding of oxygen is reduced. Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin, promoting increased oxygen delivery to tissue.
Reversible binding of phosphate and the control of conformation
The addition a removal of phosphate can cause reversible conformation change in protects. This is a common form of post-translational modification
What do protein kinase do?
Catalyse the transfer of a phosphate group to other protects.
How are phosphate groups transferred?
The terminal phosphate of ATP is transferred to specific R groups
What do protein phosphatases do?
Catalyse the reverse reaction, the removal of phosphate groups.
How is the activity of many cellular proteins regulated through phosphorylation?
Phosphorylation brings about conformational change which en affect a protein’s activity.
How can some protects be activated by phosphorylation while others are inhibited?
Adding a phosphate group adds negative charges, ionic interactions in the unphosphorylated protein can be disrupted and new ones created.
