Lecture 7 Flashcards
What is a proteome? How does it occur?
All distinct forms of a protein (caused by different post translational modifications of the same protein).
What two methods can increase diversity of the proteome? What are the two categories of protein PTM?
mRNA splicing and post translational modification(PTM)
The two categories for PTM are covalent addition of a chemical group to an amino acid side chain and covalent hydrolysis of a peptide bond in the protein.
What are the three ways PTMs may be sorted? What are three main examples of PTM?
which amino acid they affect, what chemical compound they link to the protein, the biological function generated by the PTM.
Three main examples are phosphorylation, gamma-carboxy glutamic acid and hydroxylation.
What are the main points on phosphorylation?
Can occur on Ser, Thr and Tyr side chains, typically catalysed using the kinase enzymes (dephosphorylation is done by phosphatase enzymes) using ATP and the hydroxyl group of the side chain. It causes conformational changes to the protein due to the size and charge of the phosphate, these changes affect funtion or may enable interactions. Phosphorylation and dephosphorylation is used to switch between protein conformation states to enable biological processes in a cell.
What are two examples of phosphorylation in cells?
The insulin receptor, when binded to by insulin on the extracellular (alpha subunits) causes a conformation change which activates tyrosine kinase domains on the intracellular subunits (beta subunits), specific Tyr are then phosphorylated on the beta subunits which leads to phosphorylation of insulin receptor substrate proteins, resulting in transfer of GLUT4 glucose transporter proteins to the cell membrane to enable uptake of glucose.
Sodium/potassium pump: When phosphorylated a protein conformation change occurs which allows three Na+ to bind be a translocated out of the cell, when the ion pump is dephosphorylated another protein conformation change enables two K+ to bind and be moved out of the cell. (Involves hydrolysis of ATP).
What is gamma carboxy glutamic acid (Gla)? What cofactor does it require?
A PTM that occurs only to glutamic acid in some blood coagulation proteins, it involves covalent linking of an additional carboxyl group in roughly ten to twelve amino acids, turning them to Gla and enabling formation of bi-dentate Ca2+ binding sites via the two carboxyl groups, allowing for blood coagulation proteins to interact with platelets. It requires vitamin K as a cofactor.
What is vitamin K? What does lack of it result in?
A number of compounds which have a varying number of isoprenoid units (C=C-C(C)=C). Lack of it results in bleeding disorders.
summarise the pathways of blood coagulation. Which Factors are gamma carboxylated?
Starts with the extrinsic pathway, vascular injury leading to tissue factor release which causes production of factor VII and factor IX which becomes factor IX (alpha) as well as factor X becoming factor X (alpha). The intrinsic pathway also becomes activated as the extrinsic pathway is not fast enough alone. this is activated by the factor X alpha helping to turn prothrmobin into thrombin, this causes production of factor Xi, IX and X as well as turns fibrinogen into fibrin which can then be cross linked by Factor XIII.
Factor IX, X and prothrombin are gamma-carboxylated at ten to twelve glutamic acid residues within a 40 amino acid section (creating high local densitys of bidentate chaltors for calcium ions).
What is fibrinogen, what is it made of and how is it turned to fibrin (how does it close wounds?)?
Fibrinogen consists of two alpha, two beta and two gamma subunits linked by disulfide bonds, thrombin hydrolyses parts of the fibrinogens to release fibrinopeptides and fibrin monomers which will cross link mesh to trap red blood cells and together with platelet adhesins to seal the wound.
What is hydroxylation? Where is it commonly found
A PTM which occurs mainly on the fourth position of proline (sometimes position 3), lysine can also be hydroxylated at the 5th position. It involves the addition of an OH group, increasing the ability for non covalent interactions. It is particularly abundant in collagen (the more hydroxylation the higher order collagen structure).
What is vitamin C and what is it needed for?
Vitamin C is a molecule needed by hydroxylase enzymes (that hydroxylate some proline and lysine residues in collagen), it maintains the necessary Fe in the 2+ state and a decrease in these leads to decrease in hydroxylation resulting in collagen strength decrease. Humans can’t synthesise it and hence need it in our diet.
