Enzyymes Flashcards
WHAT ARE ENZYMES
Enzymes are protein catalysts that inc. the velocity of a chemical reaction and are not consumed during the reaction they catalyse
6 enzyme reactions
- breakdown of nutrients/ molecules
- release / storage energy
3.assembly of chemical building blocks
to proteins, DNA, membranes, cells etc., - muscle contraction
- neural function
6.buffering action
What are assay of special enzymes used for
Diagnosis and prognosis
Pharmacological use of enzymes
Therapeutic value
What is enzyme specificity used for
Synthesising drugs/antibiotics
What can proteases and amylases do
Detergents
What can rennin and lactase do
Enhance nutrient value of foods
2 types of substrate specificity and examples
Absolute . Aspartic acid to fumerate using aspartase
Broad . Hexose to hexose-6-P using hexokinase
What is reaction specificity
One enzyme can catalyze only one of the various reactions a substrate can undergo
What is stereo specificity
Catalyze reactions of one stereo-isomer of a given molecule
Eg;
D - sugars (not L-)
L - amino acids (not D
What is conjugated proteins
Protein + Non protein (cofactor )
What is Holoenzyme
Apo enzyme + non-protein
2 types of enzymes
Monomeric ans multimeric
Mono vs multi meric and example
One pp chain. >1 pp chain
Ribonuclease. Lactate dehydrogenase
What is Multienzyme
complex
And 2 examples
- Many reaction catalyzing sites in same macro molecule at different sites
- Becomes inactive when units each with enzyme activity is fractionated.
- Eg;
Pyruvate
Fatty acid dehydrogenase
What does lability mean
Labile
◼ Unstable –
enzymes are proteins & are subjected to denaturation by all agents causing denaturation of
proteins.
What is catalytic efficiency
• Accelerate specific chemical reactions by decreasing activation energy.
rate by 10^3 – 10^8 times
Efficiency of an enzyme:
- given in terms of turnover number or Kcat
No of substrate converted to product /enzyme/secon
Equilibrium and enzymes
◼Enzymes increase the rate of a reaction
Equilibrium NOT altered
But equilibrium will be achieved faster
enzymes within the cell (Compartmentalization)
Isolate the substrate
and products from other competing reactions providing a favourable environment for the reactions or pathway
Mechanism of action of Enzyme Catalysis
Substrate reaches active site
Enzyme-substrate complex formed
Chemical conversion to
Enzyme product complex
Product formed
Describe active site
Is made up of several amino acids that come together as a result of specific folding of IIry and III ry structure of enzymes
5 features of active site
▪globular proteins
▪hydrophilic side chains on outer parts
▪ has specific 3D structure, shape & specific charges.
▪forms a cleft or pocket on the enzyme surface that
accepts & binds substrate.
▪Contains side chains of amino acids that participate
in substrate binding and catalysis
Action in. Active site
within the active site the substrates are brought close to one another in optimal alignment with cofactors & prosthetic gps and amino acid side chains responsible for chemical transformation in to
products.
•Active site shield substrates from water and generate an environment (polar, acid, hydrophobic or alkaline) that can differ from the surrounding cytoplasm.
how does active site facilitate catalysis
Binds the substrate & initiate conversion to transition state (TS) , stabilize the TS which allows the intermediate to be quickly converted to product
Provide catalytic gps ( amino acid side chains ) that inc the formation of TS. Eg: help catalysis by acting as acids & bases etc
Catalysis by strain - active site of enz that breaks
bonds bind substrates in an unfavourable
conformation that will help break the bond
2 models describing interaction of active site and substrate
Lock & key hypothesis (Substrate coming in and fitting into the enzyme like a key fitting into a lock)
Rigid template model - Emily fisher ( active site rigid )
Induced fit model (Active site changes to accommodate substrate – active site is flexible. Substrate induces a conformational change in the active site during binding so the final shape & form is obtained
Eg: - competitive inhibition)
6 groups of catalysts
- Oxidoreductase
- Transferases
- Hydrolyses
- Lysases
- Isomerases
- Ligases
Oxidoreductase (catalyze redox reactions)
Oxidize or reduce substrates by transfer of
hydrogens, electrons or oxygen
Ethanol + NAD+ gives ethanol + NADH + H+ using alcohol dehydrogenase
Transferases
Remove groups (not H) from substrates & transfer them to acceptor molecules (not H2O)
hexokinase ATP + glucose To glucose-6-P + ADP (ie- methyl, glycosyl or phosphoryl gps)
Hydrolases
Water participates in the breakage of covalent bonds (C-C, C-N, C-O etc) of substrate with concurrent addition of elements of water to the principles of those bonds.
Esterase ( urease) Urea + water To CO2 + 2NH3
Lyase
Catalyse cleavage of C-C, C-S and certain C-N bond
Pyruvate decarboxylase Pyruvate To Acetaldehyde + CO2
Isomerases
Rearrangement of optical or geometric isomers isomerization of substrate
Isomerase Aldose To Ketose
Ligases
join 2 molecules
Covalently link 2 molecules with subsequent breakage of a high energy bond [pyrophosphate bond (ppi)]
- forms C-C, C-N, C-O, C-S bonds
What are 6 factors affecting rate of an enzymatic reaction
- Temp
- pH
3.enzyme conc - Activators
- Inhibitors
- Substrate conc.
Arrhenius effect
Thermophilic enzyme
How does pH affect enzyme activity
-H+ ions in the medium may alter the ionization of active site & or substrates (acidic & basic side groups) and thus facilitate formation of ES complex
(change in ionic state of Enz or substrate)
- Optimal activity when maximum no. of Enz /substrate in the correct charged state.
- At extremes of pH there is no activity due to denaturation
What set activators and 2 examples
• Molecules that increase the rate of an enzyme catalyzed reaction
Eg:
metal ions
coenzymes
What is inhibitor
• Substances which stop of modify (inactivate) enzymatic activity
- change the active site
• Any substance capable of decreasing the velocity of an enzyme catalysed reaction is an inhibitor.
• Competitive / non–competitive
What is Michaelis & Menton model
• Accounts for kinetic properties of many enzymes (but not all)
What is Michaelis-Menton equation
Vo = Vmax [S]/( [S] + Km)
Describes how reaction velocity varies with substrate concentration.
When are Km and Vm constant
only at constant temperature, pH and ionic strength
Describe. Michaelis-Menton plot
V Against S
Vmax2 = Km
3 dif meanings of Km
(1) Mathematical meaning (ratio of rate constants)
K2+ k3/ k1
- Km is numerically equal to the substrate concentration at half maximal velocity
Km = Vmax / 2 (when Km = [s] ) - Km
∞ 1/affinity
- low Km – high affinity
- high Km – low affinity (Enzymes affinity to a particular substrate)
Glucose has more enzyme affinity than fructose
Lineweaver – Burk plot formation
1/ Vo vs 1/S To give straight line after manipulating michaemis menton to y = mx + c
2 purpose of Lineweaver – Burk plot
• Useful in determining Km & Vmax
• Distinguish competitive & noncompetitive
inhibitors.
Comp Vs. Non comp
- Reversible. 1. Irreversible
- binds thr n. 2. Covalent interactions
on covalent
interactions - Substrate &. • Inhi. binds to a site other
Inhibitor both than the active site.
Compete. Binding cause change in
Structure of enzyme - More inhibition =
Less affinity of
Enzyme to substrate - Higher Km
Vmax same
Examples of Competitive inhibition
- Widely used in medicine as drugs.
- Use of ethanol as treatment in methanol
poisoning
+CH3OH + NAD+
alcohol dehydrogenase
To HCHO + NADH + H+
formaldehyde
Toxic to nervous system
- inhibition of bacteria by sulphonamides
Substrate id para- aminobenzoic acid
Example of inhibitor in bacteria growth
- Inhibitor is a substrate analogue.
- p-aminobenzoic To folic acid
Folic acid is necessary for growth of bacteria. - inhibition of the enzyme inhibits folic acid formation
- Thus causing bacteria to stop growing and die.
4 clinically useful comp inhibitors
- Statins
(Atorvastatin, Simvastatin)
Inhibit HMG CoA reductase
Decrease plasma cholesterol levels - Methotrexate
Inhibit Dihydrofolate reductase
Cancer
3.Captopril & Endopril
Inhibit Angiotensin converting enzyme
High blood pressure
4.Dicumarol
Inhibit Vitamin K epoxide reductase
Anticoagulan
4 Example of non competitive inhibition
1.Heavy metals
Pb – binds with covalently with SH gps of
proteins .Lead inhibit – Ferrochelatase
insertion of Fe2+ to protoporphyrin in the synthesis of Heme
2.Cyanide - inhibits cytochrome oxidase
3.Alanine - inhibits pyruvate kinase
- insecticides – acetylcholinesterase inhibitors
Effect on M-M plot and L-B plot
Km unchanged
V max dec.
What is suicide inhibition
- related to competitive inhibition
# S and I go to active site to compete
# I is a substrate analogue
# Kinetics are similar
• However the reaction of I with enzyme is irreversible.
- I is much similar to the substrate, and the enzyme begins reacting with it.
- product can’t dissociate .
- Thus both enzyme & Inhibitor are lost.
“suicide inhibition
What is allopurinol
Drug given as treatment for gouty conditions
• Allopurinol - inhibit the enzyme xanthine oxidase
which forms uric acid from hypoxanthine.
• Allopurinol is a substrate analogue of hypoxanthine
What is gout
In the cases of high uric acid (hyperuricaemia), uric acid crystallizes in the joints. This is gout .
Cause swollen and inflamed joints
Usually
Purine catabolism to hypoxanthine to xanthine to Uric acid
How does allopurinol act
Allopurinol oxidised to oxypurinol / alloxanthine in liver and Bind to xanthine oxidase so hypoxanthine not be converted to Uric acid
What is substrate analogue
Substrate analogs, are chemical compounds with a chemical structure that resemble the substrate molecule in an enzyme-catalyzed chemical reaction.
What is passive control in enzyme regulation ?
Increase [S] - increase reaction rate
brings [S] back to a normal level by the action of enzymes of a pathway
(passive control)
What is active control of enzymes
- Is by regulation of select set of enzymes in a
pathway - These enzymes are the ones whose quantity or catalytic efficiency is slow relative to all other enzymes in a pathway (bottleneck)
= RATE LIMITING REACTION - Decreasing the catalytic efficiency or the quantity of such enzymes will quickly reduce the pathway or vice versa.
2 things that can affect catalytic efficiency
- Changes in catalytic efficiency is effected by binding of dissociable ligands
- Allosteric effectors(regulation) or by
- Covalent modification
- These are methods of controlling the activity of enzymes and thereby regulating the enzyme activity
- Rapid response (Allosteric > Covalent)
What are allosteric enzymes
- Inhibitor/activator binds to a site other than the
active site in the enzyme called allosteric site - Allosteric enzymes tend to have several subunits
- Sub units exist in 2 states (T or R) in equilibrium
Does equilibrium favour T or R form
- Equilibrium favours T form
• T (tense) form has low affinity to substrate
• R (relaxed) form has high affinity to substrate - Binding substrate to one subunit induces T to R transition (conformational change)
(binding of substrate to one active site enhances interaction between allo enz & more Substrate molecules)
• Binding of substrate to enzyme (one active site) can affect the properties of other active sites in the same enzyme
• Subunits CO-OPERATE – change in 1 subunit is transmitted to the other subunits facilitating binding S to other active sites
Display sigmoid kinetics of allosteric enzymes
Sigmoid shape
Described ( BOTTOM TO TOP )
1. T- binding difficult
2. T to R- bind easy
3. Saturation kinetic
2 types of regulatory molecules
Binding of regulatory molecules can either
enhance the activity of the enzyme
- Allosteric activation – positive modifier
OR
inhibit the activity of the enzyme
- Allosteric inhibition – negative modifier
Activator shifts T to R equilibrium
Inhibitor shifts R to T
What is homotropic effect ? =/ heterotrophic
Substrate itself serves as an effector (+ effector by converting T to R)
Example of homotropic inhibition
First reaction in pyrimidine biosynthesis
Asp transcarbamoylase (2 subunits)
Asp+ carbamoyl P To N-carbamoyl asp+ P
ATP – Activator
CTP – Inhibitor (end product)
feed back inhibition
(one type of control of allosteric enzyme48s)
Activator/ Inhibitor Heterotropic example
Phosphofructokinase I (PFK 1)
F 6 P To F 1,6 bis P
Inhibitors – ATP (high E charge),
Citrate (feed back)/ H+
Activators - ADP/AMP (low E charge)
fructose 2,6 bis P
Explain alosteric regulation of muscle phosphorylase
A low energy charge, (high concentrations of AMP), favors the transition to the R state (active) – to produce more glucose (breakdown glycogen) & thus energy
- Glycogen phosphorylase + AMP gives G6P and ATP
- Glycogen synthase is activated when high level of G6P
What is covalent modification &examples
The activity of an enzymes can be increased or
decreased by covalent modification
Addition or removal of a group to the enzyme
covalently
The addition/removal of a group is catalyzed by another enzyme
Eg:
Phosphorylation & Dephosphorylation
+P - P
Where are enzymes phosphorylated
• Many regulatory enz, have specific sites that may be enzymatically phosphorylated or dephosphorylated at serine, threonine &/or tyrosine residues
Hw r covalent mod reactions regulated
Covalent modification reactions are under hormonal control through an enzymatic cascade.
• Change the structure of enz. so the response to allosteric regulators is also altered.
Phosphorylation of glycogen synthase and phosphorylase
Glycogen synthase (controls glycogen. -P activates
More AMP and G6P
synthesis).
(Allosteric)
Glycogen phosphorylase. +P activates
More AMP.
(controls glycogen breakdown). More ATP and G6P
(Allosteric)
Exp induction and repression control
• Regulation of the amount of enzyme present
in the cell by altering the rate of synthesis.
• Enzymes needed at only one stage of development or under selected physiological conditions.
• Eg: increase key enzymes of glucose metabolism when insulin is high
• Slow process (hrs to days) compared to allosteric control
G protein cascade for glycogen phosphorylase
ATP TO CAMP TO PROTEIN KINASE A TO PHOSPHORYLASE KINASE TO PHOSPHORYLASE B TO PHOSPHORYLASE A
What are isozymes
- Multiple forms in which an enzyme may exist in an organism or in different species with the various forms differing structurally, physically, electrophoretically and immunologically, but catalyzing the same reaction.
How are enzymes used in diagnosis & 2 examples
• Many cellular enzymes are normally not present
at high concentrations in blood serum.
• When illness causes cell death, cell damage cellular enzymes spill into the bloodstream, raising levels in blood.
• The level of specific enz activity in the plasma correlates with the extent of tissue damage.
• Thus activities of enzymes are measured for diagnostic purposes in diseases of heart, liver, skeletal muscle etc.
Some enzymes/isoenzymes have high activity in only one or few tissues & increased level of these in plasma indicates the damage to the a particular tissue.
Eg:
- Alanine aminotransferase (ALT) is high in liver
- High level of ALT indicates damage to liver
What is creative kinase
ATP generation in muscle & nerves
Creatine P + ADP. To. ATP + creatine
- Increased amounts in skeletal muscle, myocardium & brain
3 isozymes and 2 subunits ( M & B )
What are 3 isozymes and functions and consequence if in blood
MM (CK3-CK-MM)
MB (CK2 –CK-MB)
BB (CK1)
skeletal muscle. cardiac
muscle. brain
cannot cross
Blood brain
barrier
entirely MM isozyme
(in plasma main)
released in cardiac
muscle damage more
than 5% of CK as CK-MB
7
What does prescience of B subunit of creative kinase indicate in blood and how is it identified ( 2 examples)
- Thus presence of B subunit in blood is indicative of cardiac muscle damage
- First enzyme to elevate in blood after Myocardial Infarction
CK-MB CK – total - Isozymes. identified- electrophoresis
ion exchange chromatography
3 uses of enzymes
- Diagnosis
2.laboratory reagents - Therapeutic use
Isoszyme in diagnosis and 5 examples
Diagnosis
Enz estimation in serum or body fluids
Eg: When illness causes cell death, cellular enzymes spill into the bloodstream, raising levels in blood.
- Alanine aminotransferase (ALT) – viral hepatitis
- Acid phosphatase - prostate cancer
- Alkaline phosphatase - bone & liver cancers
- Amylase - pancreatitis, pancreatic cancer
- LDH (lactate dehydrogenase), Creatine kinase - Myocardial Infarction- rise and fall in blood serum in specific time frames
2 examples of isozymes as lab reagents
Glucose oxidase used for estimation of glucose in the blood
Urease used for estimation of urea in blood etc.
2 therapeutic uses of isozymes
amylase /lipase /protease –replacement therapy in pancreatic insufficiency
hyaluronidase – depolymerise ground substance
