6 Enzymes Flashcards
1
Q
What is the definition of an enzyme
A
- A biological catalyst which speeds up the rate of reaction without itself being changed
2
Q
In what ways can Enzymes be involved in disease
A
1 - Any malfunction in enzyme activity disrupts homeostasis
2 - DNA mutations resulting in underproduction/deletion in a single critical enzyme can be fatal
3- A single amino acid substitution could destabalise protein structure and disrupt the binding site
4- Mutations in enzymes that repair DNA and control cell cycle can result in cancer
3
Q
Explain the symptoms and cause behind the genetic condition phenylketonuria
A
- cause by a mutated enzyme (phenylalanine hydroxylase)
- which reduces or stops the metabolism of phenylalanine
- phenylalanine is toxic in excess amounts
- build of can cause seizures, behavioural problems, eczema
4
Q
Describe the general structure of enzymes
A
- globular proteins with a binding site and a catalytic site which are all part of the active site
5
Q
what is the job of the catalytic site
A
- it reduces chemical activation energy
6
Q
what is the job of the binding site
A
- it binds and orients the substrate into the correct position
7
Q
What features of the binding site enable it to bind with the substrate
A
- The active site is highly specific
- It is a non-polar environment that enhances binding by multiple weak forces: hydrogen bonds, hydrophobic interactions, van der waals, electrostatic and reversible covalent bonds
8
Q
what are the 2 theories of enzyme binding and explain
A
- Lock and key: the active site is rigid and fixed
- Induced fit model: the binding of the substrate to the active site induces a conformational change in shape to fit around the substrate
9
Q
What features determine substrate specificity
A
- amino acid residues
- complementary shape, charge and hydrophobic interactions with the active site
10
Q
What is the purpose of the allosteric site
A
- to regulate the activity of the enzyme
11
Q
explain how the allosteric site can inhibit the enzyme
A
- Binding of a substrate to the allosteric site can induce a conformational change to the active site
- This change can inhibit or activate the enzyme
12
Q
What is an enzyme cofactor
A
- This can be an inorganic molecule such as metals ions, or an organic compound such as NAD+ or an amino acid
- some enzymes use cofactors to optimise their activity
13
Q
What is the name given to the type of enzyme before binding to a cofactor and after
A
Apoenzyme (inactive) + cofactor = Holoenzyme (active)
14
Q
What is a co-enzyme
A
- a coenzyme is a compound that is transiently bound to the enzyme, and can change/ be altered during an enzyme reaction
- They area often vitamin precursors and a deficiency of them can cause disease
15
Q
What is a prosthetic group
A
- A metal or coenzyme covalently bonded to the enzyme and is not altered during the reaction
16
Q
Explain how scurvy is a disease relating to coenzymes
A
- scurvy is caused because of deficiency of vitamin C (ascorbic acid)
- which is needed as a cofactor for enzymes to stabilise collagen
- lack of ascorbic acid results in lethargy, bloody gums, poor wound healing, sores and other symptoms
17
Q
How are enzymes named
A
- the prefix denotes the substrate being broken down
- the -ase indicates its and enzyme
18
Q
List the major different catagories/types of enzymes
A
- Oxidoreductase
- Transferase
- Hydrolases
- Lyases
- isomerase
- ligases
19
Q
Explain the roles of each of these types of enzymes
- Oxidoreductase
- Transferase
- Hydrolases
- Lyases
- isomerase
- ligases
A
- Oxidoreductase: Transfer oxygen or hydrogen atoms across substrates
- Transferase: Transfer a functional group between substrates
- Hydrolases: catalyse hydrolysis
- Lyases: Addition or removal of a group to form a double bond
- isomerase: transfer of groups within a molecule
- ligases: bond formation coupled with ATP hydrolysis
20
Q
Describe the graph of an exergonic reaction
A
- The reactants have high energy
- A small activation energy is needed to start the reaction
- After the transition state the products are formed and have much less energy
- overall reaction is -Delta G and these types can be spontaenous
21
Q
How do lysozymes destroy most pathogens
A
- They break down the peptidoglycan wall within the cell wall
22
Q
What is a coupled reaction
A
- When an more endergonic reaction is paired with a less exergonic reaction so that both reactions occur and the net Gibbs free energy is negative, energetically favourable
23
Q
Give an example of a coupled reaction
A
Any reaction that involves the hydrolysis of ATP->ADP as this drives the exergonic reaction as its so endergonic
24
Q
How can enzymes reduce the activation energy, 4 ways
A
- Catalysis by approximation: bringing the reactants together lowers the activation energy
- Metal ion catalysis: having cofactors can lower the Ea
- Covalent catalysis: the substrate temporarily becomes covalently bonded to the enzyme, this lowers the Ea
- Acid-base catalysis: when the enzyme uses its acidic/basic environment in the active site for catalysis
25
What is the michaelis constant and its units
- Km
- This is a measure of the affinity of an enzyme for its substrate
- Units (Molar) or concentration
26
How can you calculate the michaelis constant
- plot the graph for [Substrate] against reaction rate (Velocity)
- Find 1/2 Vmax and interpolate to the [Substrate] = Km
27
What does a low michaelis constant indicate
The enzyme has a higher affinity for the substrate
28
How does temp affect an enzyme
- initially an increase of temp increases the kinetic energy and ror, but beyond optimal temp the ror declines rapidly as the enzyme denatures and weak bonds in the protein break changing the shape of the active site
29
Hoe does pH affect an enzyme
- small pH changes reduce activity due to ionisation of groups in the active site
- Large pH changes cause denaturing
30
How can the rate of reaction be measured in an enzymes experiment
- by monitoring the rate of substrate disappearance or product increase
- change in light absorbance
- change in colour
- chromatography
- radiography
31
What is a substrate analogue
- a chemical compound that is similar enough in structure to a substrate that it can bind to the enzyme active site
32
Name the different categories of enzyme inhibition and their sub-categories
- Non specific or denaturing
| - specific and reversible and irreversible: competitive, non-competitive, uncompetitive
33
How do reversible inhibitors work
- they bind to the enzyme via weak non covalent bonds, hydrophobic interactions, hydrogen/ioninc bonding
- so the enzyme remains chemically unchanged
34
- how do competitive inhibitors work and how does this effect Km
- they have a similar shape to the substrate and bind to the active site of the enzyme blocking it
- Km increases because the ror decreases and the enzyme affinity for the substrate is reduced
35
- How do non-competitive inhibitors work and how does this effect the Km
- They bind to the allosteric site of an enzyme causing a conformational change in the shape of the active
- Km remains unchanged because Vmax is reduced for this reaction as well as the ror
36
- How do un-competitive inhibitors work and how does this effect the Km
- they bind to the enzyme substrate complex blocking and inhibiting catalysis
- Km is reduced as Vmax is drastically reduced
37
How is the rate of glycolysis regulated by enzymes
- The second product in glycolysis (GP) allosterically inhibits hexokinase the enzyme that breaks down glucose slowing down the first step if there are too much of the product
- A high concentration of ATP allosterically inhibits 2 enzymes in glycolysis (PFK and Pyruvate kinase)
38
What is cooperative binding and give an example
- when there is a conformation change to another binding site increasing its affinity to the substrate after the first site has bound
- eg haemoglobin
39
how does the shape of a curve plotting ROR against t compare when applied to a normal enzyme and an allosteric enzyme
- allosteric enzymes have an S shaped curve rather than a regular enzyme curve
- this shows that they are more sensitive to small changes in [substrate] and there is a rapid increase in ROR over a smaller [substrate] range
40
What is an allosteric enzyme
- a multi-subunit enzyme with more than one binding site
| - eg haemoglobin
41
How can enzymes be modified?
- a process called reversible covalent modification where other enzymes add or subtract a phosphate group from the enzyme changing the tertiary structure
- protein kinase phosphorylates (adds)
- protein phosphatase dephosphorylates (removes)
42
What is proteolytic activation
- where an inactive enzyme called a zymogen or proenzyme is activated by hydrolysis of a peptide bond in it
43
What is a labile enzyme
- these are enzymes with a very short half life, normally involved in metabolism and naturally breakdown over time
