Highlights Catalytic Strategies (continued)
1. Restriction enzymes are paired with a methylase in bacterial cells. The methylase puts a methyl group on the same sequence the restriction enzyme would otherwise cut. When cellular DNA is protected in this way, the restriction enzyme cannot cut the cellular DNA, but it can cut invading viral DNA if it gets to it before the methylase does.
2. Restriction enzymes bind to DNA and "slide" along the double helix. When they reach the sequence they cut at (recognized by hydrogen bonds), the DNA is bent and a magnesium ion is allowed into the complex to facilitate the activation of water to nucleophilically attack the phosphodiester bond, cleaving it.
3.Myosin is a protein that undergoes a significant shape change upon hydrolysis of ATP. This action allows it to move along actin filaments and facilitates muscular contraction.
Highlights Allostery and Regulation
1. Aspartate transcarbamoylase (ATCase) is an enzyme that catalyzes the first step in pyrimidine biosynthesis (aspartate + carbamoyl phosphate <=> N-carbamoylaspartate). This enzyme is allosterically regulated in both a positive and negative fashion and also responds to the binding of the substrate (aspartate) to it.
2. CTP, the end product of pyrimidine biosynthesis, inhibits the enzyme,whereas ATP (a purine and an indicator of high energy) activates the enzyme. This phenomenon - where the end product of a metabolic pathway inhibits the first enzyme in the pathway - is known as feedback inhibition. Feedback inhibtion is mediated allosterically - when a small molecule binds to a protein and affects the protein's activity.
3. ATCase has 12 subunits - 6 catalytic and 6 regulatory. The smaller regulatory subunits bind CTP, but not the catalytic subunits.
4. Binding of CTP to the regulatory subunits of ATCase causes the enzyme to stabilize (lock) in the T state (tight, less reactive state). In the T state, the quaternary structure of the enzyme the enzyme exhibits reduced affinity for substrate. In the opposite state, the R state (relaxed state, more reactive state), the enzyme has increased activity and a higher affinity for substrate. ATP stabilizes the R state of the enzyme.
5. In the absence of ATP and CTP, the enzyme can freely flip between the T and R states, but the T state tends to predominate.
6. If one removes all of the ATP and CTP from the enzyme and starts adding increasing amounts of the enzyme's normal substrate (aspartate) and then measures the reaction rate (velocity), one discovers a sort of sigmoidal plot, which indicates that the enzyme is actually changing as more aspartate is added to it. The actual change is a flip from the T state to the R state stabilized by the aspartate.
7. You should be familiar with the effects of ATP, CTP and increasing aspartate on ATCase and where they bind on the enzyme to exert their effects.
8. A manmade artificial substrate, known as PALA, binds to ATCase and inhibits the enzyme, but interestingly locks it in the R state. Though the enzyme can't catalyze a reaction when bound to PALA, it is clear that its form changes, again indicating that enzymes are changed by the binding of substrate and that T and R states exist.