Module 1.2 - Protein function, enzyme kinetics and regulation Flashcards
What is a kinase?
Catalyses the phosphoryl transfer from one molecule (usually ATP) to another e.g. Hexokinase
What is a phosphorylase?
Catalyses the covalent addition of inorganic phosphate (Pi) to a molecule e.g. Glycogen phosphorylase. It’s main role is to cleave a bond.
What is a Phosphatase?
Catalyses the cleavage of a phosphate to yield the dephosphorylated product and Pi, e.g. Glucose-6-phosphatase (synthesis of glucose)
What is a dehydrogenase?
catalyses an oxidation/reduction reaction commonly using NADH/NAD+, NADPH/NADP+ or FADH2/FAD as cofactors; e.g. Glyceraldehyde-3-phosphate dehydrogenase
What is a mutase?
Catalyses the shift of a phosphoryl group from one atom to another within the same molecule e.g. Phosphoglycerate mutase
What is an isomerase?
Catalyses the conversion of one isomer to another; e.g. Triose Phosphate Isomerase
What is a hydratase?
Catalyses the addition/removal of water, e.g. enolase
What is a synthase?
Catalyses the synthesis of a product, e.g. citrate synthase
What is the function of myoglobin?
The storage of oxygen in muscles and the release of oxygen when rapidly contracting muscle needs energy.
Describe the tense state of haemoglobin
The tense state (T state) has a lower affinity for oxygen, and there are more interactions, and it is more stable
Describe the Relaxed state of hemoglobin
The relaxed state (R state) has a higher affinity for oxygen, fewer interactions, and more flexibility. The binding of oxygen triggers a conformational change from the T state to the R state.
Describe the Bohr effect
Actively metabolising tissues generate H+, lowering the pH of the blood near the tissues relative to the lungs. Hb affinity for oxygen depends on the pH. At lower pH (high concentration of H+) the affinity of Hb for O2 is decreased because H+ stabilises Hb in the T state. This helps offload O2 from Hb to the tissues. It also protonates His HC3, which then forms a salt bridge with Asp FG1. The pH difference between the lungs and metabolic tissues increases the efficiency of the O2 transport.
How is CO2 exported through haemoglobin?
15-20% of CO2 is exported in the form of a carbamate on the amino terminal residues of each of the polypeptide subunits. The formation of a carbamate yields a proton that can contribute to the Bohr effect. The carbamate forms additional dalt bridges, stabilising the T state. Release of CO2 in the lungs favours the R state.
How does BPG regulate O2 binding to haemoglobin?
BPG is a negative allosteric regulator of Hb function. Present at mM concentrations in red blood cells (produced from an intermediate in glycolysis). It is a small negatively charged molecule which binds to the positively charged central cavity of Hb and stabilises the T states. Decreases the affinity of Hb for O2
What are enzymes, and how do they work?
Enzymes are biomolecules (e.g. proteins) that have a distinct 3-D structure and employ catalytic mechanisms such as weak interactions, acid-base, covalent and metal ion catalysis. Enzymes provide a specific environment, i.e. active site, for a given reaction to proceed rapidly compared to the uncatalysed or spontaneous reaction. The active sites of enzymes are lined with functional groups (usually from amino acids) that bind the substrate and catalyse the chemical transformation to product. Enzymes affect reaction rates, but not equilibria.
How do enzymes reduce the activation energy and accelerate rates of reaction?
They bind substrates in the correct orientation relative to the active groups. By providing catalytically active groups (side chains, acids, bases, metal ions). Also, by stabilising the transition state.
What is the turnover number (kcat)?
The number of molecules of substrate converted to product (S to P) per unit time per enzyme molecule saturated with substrate i.e. when [ES] = [Et]
Define what an irreversible inhibitor does
They bind covalently to the active site, destroy a functional group essential for enzyme activity, or form a stable noncovalent complex with the enzyme, ‘suicide inhibitors’.
Define what a reversible inhibitor does
They bind reversibly to enzymes and inhibit the enzymes and inhibit the enzyme either by competitive, uncompetitive or mixed modes of inhibition and then dissociate for the enzyme to be active again.
What are allosteric enzymes?
- Allosteric enzymes often regulate metabolic pathways by changing activity in response to changes in the concentration of molecules around them
- Allosteric enzymes are regulated by compounds called ‘allosteric modulators’ or ‘allosteric effectors’
- ‘Positive modulators’ activate and ‘negative modulators’ inhibit allosteric enzymes
Modulators bind reversibly and non-covalently to the enzyme - they can ‘come and go’
What is ATCase, and how is it modulated?
ATCase catalyses the first step in the E. coli pathway to produce the nucleotides UTP and finally CTP. When present at high levels, CTP inhibits ATPase (it’s a negative modulator). High ATP levels in the bacteria indicate growth of the cell and the need for more CTP, therefore, ATP is a positive modulator of ATCase.
