Enzymes Flashcards
1
Q
What are the 4 main differences between enzymes and ordinary chemical catalysts
A
- Higher reaction rates- at least several orders of magnitude greater
- Milder reaction conditions- temp below 100 degrees, nearly neutral pH’s, atmospheric pressure. Chemical catalysis often require elevated temps and pressures and extreme pH
- Greater reaction specificity- rarely have side products and go to completion
- Capacity for regulation- activity varies in response to concentrations of substances other than their substrates- allosteric control covalent modification and variation of amount of enzyme synthesised.
2
Q
What do catalysts do
A
- Speed up chemical reactions
- Don’t change equilibrium constants
- Recycled, they are not consumed in reaction
- Are not reagents or co-factors
3
Q
Give an example of chemical catalysis
A
- Hydrogenation of ethene on a metal surface
a) Surface chemo-adsorption of H2
b) Surface chemo-adsorption of ethene
c) Electrophilic addition
d) Rearrangement
e) Desorption of ethane product
4
Q
Compare Kcat/Kuncat values for chemical and enzyme catalysis
A
- For chemical catalysis Kcat/Kuncat = 10^1 - 10^4
2. For enzyme catalysis Kcat/Kuncat = 10^4 - 10^17
5
Q
Name 3 theories of enzyme binding
A
- Lock and key hypothesis
- Induced fit
- Transition state stabilisation model
6
Q
Briefly describe the lock and key hypothesis
A
- Binding site is rigid and complementary to the ligand’s geometry
- The specificity of an enzyme for its substrate arises form their geometrically complementary shapes
- The shape of the active site is determined by the quaternary and tertiary structure of a protein
7
Q
Briefly describe the induced fit model
A
- The ligand and binding site are flexible
- Binding induces a conformation change
- Certain enzymes catalyse similar reactions
- Induced fit suggests that the active site will interact with the substrate and adapt to it to make the perfect fit
- Hexokinase example of induced-fit
8
Q
Generally what does a substrate binding site consist of
A
- An indentation or cleft on the surface of an enzyme molecule that is complementary in shape to the substrate (geometrically complementarity)
- Amino acid residues that form the binding site are arranged to interact specifically with the substrate in an attractive manner (electronic complementarity)
- Molecules which differ in shape or functional group distribution from the substrate cannot form enzyme-substrate complexes that lead to the formation of products
9
Q
What is stereo-specificity
A
- Stereo-specificity is a description of the reaction path, not the selectivity for substrates or products
- Enzymes are highly specific both in binding chiral substrates and in catalysing their reactions
- This is because enzymes are chiral so form asymmetric active sites
- This is termed ‘enantio-selective’
- Enzymes are absolutely stereo-specific in the reactions they catalyse.
- A substrate of the wrong chirality will not fit into an enzymatic binding site
10
Q
Give an example of stereospecificity
A
- E.g alcohol dehydrogenase of yeast
- Ethanol is pro-chiral
- The ADH active site determines the ethanol binding geometry
- ADH transfers the pro-R hydrogen of EtOH to the NAD+
11
Q
What is geometric specificity/ Regiospecificity
A
- More strict requirement than stereospecificity
- Selective about identities of chemical groups on their substrates
- Enzymes vary a lot in their level of geometric specificity
- A few enzymes are absolutely specific for only one compound
- Most catalyse for reactions of a small range of related compounds e.g. YADH catalyses oxidation of primary and secondary alcohols
- Many enzymes particularly digestive enzymes are very permissive in their range of acceptable states
12
Q
Define cofactor
A
- Small molecules required by some enzymes during catalysis
- Some cofactors are transiently associated with a given enzyme molecule so they function as co-substrates
13
Q
Define coeznymes
A
- Organic cofactors
- Are chemically changed by the enzymatic reactions in which they participate in
- So must be returned to original state to complete catalytic cycle
14
Q
Define prosthetic groups
A
- Cofactors which are permanently associated with their protein often by covalent bonds e.g heme prosthetic group of heamoglobin
15
Q
Define holoenzyme
A
- A catalytically active enzyme-cofactor complex
16
Q
Define apoenzyme
A
- The enzymatically inactive protein resulting from the removal of a holoenzyme’s cofactor
17
Q
Show equation linking apoenzyme and holoenzyme
A
- apoenzyme (inactive) + cofactor holoenzyme (active)
18
Q
Describe how vitamins are important for enzyme action
A
- Many organisms are unable to synthesise certain portions of essential coenzymes and therefore these substances must be present in the organism’s diet- vitamins
- Vitamins in the human diet which are precursors are water-soluble
- Lipid-soluble vitamins A and D are not components of coenzymes
19
Q
Describe how vitamin B1 (thiamine) acts as a coenzyme precursor
A
- Coenzyme= thiamine pyrophosphate
- Coenzyme function= decarboxylation reactions
- Human deficiency disease= Beriberi
20
Q
Describe how vitamin B2 (Riboflavin) acts as a coenzyme precursor
A
- Coenzyme= flavin coenzymes
- Coenzyme function= oxidation reduction reactions involving 2 hydrogen atoms
- No disease
21
Q
Describe how vitamin B3 (niacine) acts as a coenzyme precursor
A
- Coenzyme= NAD+
- Coenzyme function= oxidation-reduction reactions involving the hydride ion (H−)
- Human deficiency disease= pellagra
22
Q
Describe how vitamin B6 (pyridoxine) acts as a coenzyme precursor
A
- Coenzyme= pyridoxal phosphate
- Coenzyme function= variety of reactions including the transfer of amino groups
- Human deficiency disease= N/A
23
Q
Describe how vitamin B12 (cyanocobalamin) acts as a coenzyme precursor
A
- Coenzyme= Cobalamin coenzymes
- Coenzyme function= Intramolecular rearrangement reactions
- Human deficiency disease= pernicious anemia
24
Q
Describe how vitamin Biotin acts as a coenzyme precursor
A
- Coenzyme= biotin
- Coenzyme function= carboxylation reactions
- Human deficiency disease= N/A
25
Q
Describe how vitamin Folic acid acts as a coenzyme precursor
A
- Coenzyme= tetrahydrofolate
- Coenzyme function= carrier of one-carbon units such as the formyl group
- Human deficiency disease= anemia
26
Q
Describe how vitamin Pantothenic acid acts as a coenzyme precursor
A
- Coenzyme= coenzyme a
- Coenzyme function= carrier of acyl groups
- Human deficiency disease= N/A
27
Q
Describe how vitamin c (Ascorbic acid) acts as a coenzyme precursor
A
- Coenzyme= None
- Coenzyme function= antioxidant; formation of collagen, a protein found in tendons, ligaments, and bone
- Human deficiency disease= scurvy
28
Q
What are two ways that an organism can regulate catalytic activities of its component enzymes
A
- Control of enzyme availability- amount of a given enzyme in a cell depends on both its rate of synthesis and its rate of degradation
- Control of enzyme activity- Enzymes catalytic activity may be directly regulated through conformational or structural alterations
29
Q
What are the different types of regulation
A
- Enzyme regulation can be positive or negative- Activation or Inhibition
- It can involve non-covalent or covalent interactions- Covalent binding of the regulatory molecule and Non-covalent interaction of the regulatory molecule e.g. Ionic, hydrophobic, van der Waals forces
- It can be reversible- Non-covalent and covalent
- It can be irreversible- Post translational modifications, protein cleavage, irreversible regulatory molecule binding
30
Q
Describe non-covalent regulation
A
- E + R ER
- Remove R and activity returns to normal
- It is highly specific- So only the target enzyme is affected
- Two main types of non-covalent regulator- Simple inhibitors and Allosteric regulators
