3) Biochemical Basics Flashcards
(42 cards)
Outline the idea of the lock and key model
Complementary 3D surface that recognises the substrate
- substrate binds through hydrophobic, electrostatic interactions and H bonds
- binding can be prevented by steric hindrance and charge repulsion
Outline the idea of the induced fit model
As substrates bind, enzymes undergo conformational change
- side chains of AA (active site) reposition
- binding interactions increase
(Not a rigid lock but a dynamic surface)
What is the structure of the active site
A cleft / crevice formed by polypeptide chains
- the 3D arrangement permits reacting substrates to approach each other
What is a transition state complex
An unstable high energy complex with strained electronic configuration
‘Activation energy’ of formation is reduced compared to the non-catalysed reaction
What are the 2 general classes of coenzymes
1) activation - transfer:
participates directly in catalysis by forming a covalent bond with the substrate. Performed by coenzymes function group. Separate portion binds to the enzyme
2) oxidation-reduction eg NAD+, FAD+ :
Coenzyme is involved in the oxidation from compound coenzyme is involved in the reduction of a compound
What is lactate dehydrogenase
Catalysed the transfer of electrons from lactate to NAD+
Uses coenzyme NAD+
-synthesised from vitamin niacin and ATP
Adenosine diphosphate portion binds to enzyme and alters conformation
Functional group of NAD+ found in nicotinamide ring
What is the role of metal ions in catalysis
Positive charge metal ions act as electrophoresis and can assist in substrate binding or stabilise anions
Can accept or even donate electrons in oxidation-reduction reactions
What is the role of alcohol dehydrogenase
Transfers electrons from ethanol to NAD+
- generates acetaldehyde and NADH
- active site contains activated serine
- negative charge stabilised by Zn2+
What are isoenzymes
Enzymes that differ in AA sequence but catalyse the same chemical reaction.
May show different kinetic parameters (different Km and Vmax)
What is a multi enzyme complex
Enzymes that promote consecutive reactions in a metabolic pathway eg the pyruvate dehydrogenase complex consists of 3 enzymes
- pyruvate dehydrogenase
- dihydrolipoyl transacetlyase
- dihydrolipoyl dehydrogenase
What are the advantages of multi enzyme complexes
- transit time via diffusion is reduced
- less interference: products are acted upon by the correct enzyme
What are the 3 categories that enzymes in serum are divided into
- serum specific enzymes: normal location eg enzymes involved in blood coagulation
- secreted enzymes: pancreatic lipase or salivary amylase
- non serum specific enzymes: no physiological role in serum, released due to cell turnover, morphological changes
How does ischaemic heart disease form
Heart cell functioning is dependent on oxygen and this is compromised by cholesterol-rich atheromatous plaques. Blockages lead to:
- temporary ischaemia and ‘angine pectoris’
- myocardial infarction
- irreversible damage to cardiac cells
In an enzyme catalysed reaction what is the difference between the pre ready state and the steady state
In the pre-ready state there is excess substrate so for a few hundred milliseconds the product formation gradually builds up
Then in the steady state reaction rate and intermediate concentration change relatively slowly
What does the Km value show
At high concentrations [S]»Km all active sites are occupied, reaction rate is independent of [substrate], no more enzyme substrate complex can be formed. 0 order / saturation kinetics
At low concentrations [S]<
At a hypothetical infinitely high substrate concentration what are the characteristics of enzymes
- all enzyme molecules contain bound substrate
- reaction rate is at Vmax
- varies depending on enzyme amount used
What is Km
The michaelis constant
The substrate conc at which the initial rate is 1/2 Vmax
Enzyme velocity is most sensitive to changes in substrate conc just below Km
Knowing Km permits calculation of [substrate] required to saturate all active sites
Low Km= high substrate affinity
High Km= low substrate affinity
What is the Kd constant
Kd= k-1 / k1
How do the different Isozymes of hexokinase help with their respective jobs
Hexokinase I (Isozyme in RBC) has a Km of 0.05M (Vmax = low) so will permit glycolysis even in very low blood [glucose]
Glucokinase (found in liver) has a Km of 5-6 mM (Vmax = high) and so permits the storage of glucose as liver glycogen but only when glucose is in excess of energy needs.
What is a competitive inhibitor
Competes with the substrate at the substrate recognition site as it has a close structural analog.
Can be overcome by increasing the substrate concentration.
Inhibitors increase the apparent Km but have no effect on Vmax
How do statin drugs (antihyperlipidemic agents) work
- inhibit rate limiting step of cholesterol biosynthesis
- hydroxymethylglutaryl- CoA reductase
- structural analogs of substrate
What is non-competitive inhibition
Lowers enzymes Vmax as it lowers [active enzyme]
Non-comp inhibitors do not interfere with E to S binding so Km is not affected
What is uncompetitive inhibition
Can only bind to the E-S complex and not to free enzyme.
-inhibitor binding must be located either at a site created by conformational change or to a substrate
- creates a dead end complex
Cannot be overcome by increasing substrate conc
What is irreversible inhibition
Inhibitors such as carbon monoxide bind via covalent bonds to enzyme.
Cannot be removed by dialysis
Reduces amount of enzymes available for reaction.
Can target functional group or metal atom of active site
