Week 2 Flashcards
Enzymes, regulation, inhibition, activation, catalysis
Explain the activation energy. What does the size of the activation energy dictate?
Activation energy is an energy “barrier” that needs to be overcome for a reaction to occur, in both exergonic and endergonic reactions. The size of the activation energy dictates the rate of the reaction.
Name the four general strategies of enzyme catalysis which lower the activation energy.
Straining the substrate molecule, positioning substrates in close proximity, redistribute charge, and covalently bond with the substrate
Explain the specificity of an enzyme’s active site
There is typically a close shape match between the active site and substrate, like a lock and key. The shape of the active site can change when the substrate enters the active site, an induced fit.
Explain the 6 steps of the catalytic cycle of an enzyme
- Substrates enter the active site and enzyme enfolds the substrates with induced fit.
- Substrates are held in the active site by weak interactions.
- The active site lowers the activation energy (Ea) and speeds up the reaction.
- Substrates are converted into products.
- Products are released.
- Active site becomes available again for new substrates.
What happens to reaction rates when temperatures are BELOW optimum?
Low temperatures cause there to be fewer collisions between enzymes and substrates, meaning the reaction rate is lower.
What happens to the reaction rate in temperatures ABOVE optimum?
High temperatures can cause enzymes to denature and the active site can lose its shape that allows specific reactions, meaning the reaction rate is lower.
What happens to the reaction rate when the pH is above OR below optimum?
Residues may be protonated or deprotonated which decreases their activity. The reaction rate is lower.
What are cofactors in catalysis and what are the two types?
Cofactors are required for catalysis in some enzyme activity. Cofactors can be inorganic ions or complex organic molecules (coenzymes).
Where does a competitive enzyme inhibitor bind and how does this affect catalysis?
It binds to the active site and competes with normal substrates, so normal substrates cannot bind to the active site, therefore decreasing catalysis.
Where does a non-competitive enzyme inhibitor bind and how does this affect catalysis?
It binds away from the active site, on the allosteric site. This in turn changes the shape of the active site so catalysis cannot occur.
Explain allosteric regulation
Allosteric regulation happens when molecules bind to the allosteric site on an enzyme (not the active site) to either activate or inhibit it. This helps control metabolic pathways, often through feedback inhibition, and can also involve cooperativity, where binding at one site affects other active sites in multi-subunit enzymes. Allosteric control is very fast.
Explain feedback inhibiton
The end product of a metabolic pathway inhibits an enzyme that catalyses an earlier reaction in the pathway. As the concentration of the product increases the enzyme will be switched off, and when that is used again the enzyme will be switched back on.
Explain genetic regulation
The end product of a metabolic pathway can inhibit the expression of an enzyme that catalyses reactions in a metabolic pathway. This involves repressor proteins. Synthesis can be blocked and unblocked.
Explain covalent regulation and the two proteins involved in this
Enzymes can be phosphorylated or de-phosphorylated, which can switch them on or off, depending on the enzyme. Kinases transfers a phosphate from ATP to an enzyme, and phosphatase removes a phosphate.
Explain compartmentalising as a means of metabolic control
Having enzymes in a particular location in cells, where the reactions need to occur.
Explain the difference between reversible and irreversible inhibitors
Reversible inhibitors bind temporarily to an enzyme and can be removed for the enzyme to regain activity - this includes competitive and non-competitive inhibitors.
Irreversible inhibitors permanently bind to an enzyme, usually by covalent bonds, and inactivates the enzyme - these are often toxic.
What type of reaction is respiration?
An exergonic, redox reaction
Where does aerobic respiration occur in eukaryotes?
The cytosol and mitochondria
Where does aerobic respiration occur in prokaryotes?
In the cytosol and plasma membrane
What are the four different stages of cellular respiration?
Glycolysis, pyruvate oxidation, the citric acid cycle and oxidative phosphorylation
What is the purpose of the cristae in the inner membrane of the mitochondria?
To increase the surface area of the inner membrane
What is the space between the inner and outer membrane of the mitochondria called? What is there a high concentration of here?
The intermembrane, which has a high concentration of protons
Where does glycolysis occur?
In the cytosol
What are the first five reactions of glycolysis called?
The energy investment phase
What are the last five reactions of glycolysis called?
The energy payoff phase
How many ATPs are yielded from glycolysis?
2 ATPs per glucose
How many NADH are yielded from glycolysis?
2 NADH per glucose
What conversion occurs during the energy investment phase of glycolysis?
Glucose is converted to two glyceraldehyde 3-phosphates
What conversion occurs during the energy payoff phase of glycolysis?
Two glyceraldehyde 3-phosphates are converted to two pyruvayes
Why is glucose converted to glucose 6-phosphate (phosphorylated) at the start of glycolysis?
Because it increases the reactivity and free energy, which makes reactions further down the pathway easier.
What is the phosphorylation of glucose during glycolysis catalysed by?
Hexokinase
When the two G3P are oxidised at the start of the energy payoff phase of glycolysis where are the electrons passed to?
NAD+
Explain susbtrate-level phosphorylation
Some ATP is made by direct transfer of a phosphate group from an organic substrate to ADP by an enzyme
How are the ATPs in glycolysis produced?
By substrate-level phosphorylation
What is the key regulatory enzyme in glycolysis?
Phosphofructokinase
What is phosphofructokinase activated and inhibited by?
Activated by AMP (cell low in energy) and inhibited by ATP and citrate (cell high in energy)
