Enzymes are protein catalysts found in cells and tissues. They are responsible for chemical reactions in the body and can be detected in serum to diagnose diseases. Increased enzyme levels in serum may indicate tissue damage or certain disease states. Common enzymes measured include alkaline phosphatase, acid phosphatase, amylase, lipase, SGPT and SGOT which can help diagnose diseases of the bones, prostate, pancreas and liver. Enzymes function as biological catalysts by lowering the activation energy of reactions and increasing their rates without being consumed in the process. They are highly specific and their activity can be affected by factors like pH, temperature, substrate and inhibitor concentrations.
A protein synthesis inhibitor is a substance that stops or slows the growth or proliferation of cells by disrupting the processes that lead directly to the generation of new proteins. All of the antibiotics that target bacterial protein synthesis do so by interacting with the bacterial ribosome and inhibiting its function. The ribosome might not seem like a very good target for selective toxicity, because all cells, including our own, use ribosomes for protein synthesis.The good thing is that bacteria and eukaryotes have ribosomes that are structurally different. Bacteria have so-called 70S ribosomes and eukaryotes have 80S ribosomes. No, not '70s and '80s ribosomes, although that would be pretty entertaining. The S stands for 'Svedberg unit,' and it refers to the rate at which particles sediment down into the tube during high-speed ultracentrifugation. Basically, it tells us about the ribosome's molecular weight and shape.
70S and 80S ribosomes are different enough that antibiotics can specifically target one and not the other. Let's take a closer look at the bacterial 70S ribosome and see where some different kinds of antibiotics act on it. Remember that ribosomes are made of RNA and protein and that they have two subunits, one large and one small.
The bacterial 70S ribosome's subunits are the 50S subunit and the 30S subunit. Yes, I know, 50 + 30 = 80, not 70, but this is not a math mistake. Using the Svedberg unit to measure ribosomes means that things don't always add up perfectly, because rates of sedimentation are not additive like molecular weights are.
Before we get into the specifics of how antibiotics inhibit bacterial ribosomes, let's briefly review how ribosomes work. First, a tRNA loaded with a particular amino acid enters the ribosome at the A site. The tRNA's anticodon has to match the codon, or group of three nucleotides on the mRNA. Then, at the P site of the ribosome, a peptide bond forms between the previous amino acid and the new amino acid. Finally, the empty tRNA exits at the E site. This process repeats for the whole length of the mRNA, and the polypeptide chain continues to grow.
A protein synthesis inhibitor is a substance that stops or slows the growth or proliferation of cells by disrupting the processes that lead directly to the generation of new proteins. All of the antibiotics that target bacterial protein synthesis do so by interacting with the bacterial ribosome and inhibiting its function. The ribosome might not seem like a very good target for selective toxicity, because all cells, including our own, use ribosomes for protein synthesis.The good thing is that bacteria and eukaryotes have ribosomes that are structurally different. Bacteria have so-called 70S ribosomes and eukaryotes have 80S ribosomes. No, not '70s and '80s ribosomes, although that would be pretty entertaining. The S stands for 'Svedberg unit,' and it refers to the rate at which particles sediment down into the tube during high-speed ultracentrifugation. Basically, it tells us about the ribosome's molecular weight and shape.
70S and 80S ribosomes are different enough that antibiotics can specifically target one and not the other. Let's take a closer look at the bacterial 70S ribosome and see where some different kinds of antibiotics act on it. Remember that ribosomes are made of RNA and protein and that they have two subunits, one large and one small.
The bacterial 70S ribosome's subunits are the 50S subunit and the 30S subunit. Yes, I know, 50 + 30 = 80, not 70, but this is not a math mistake. Using the Svedberg unit to measure ribosomes means that things don't always add up perfectly, because rates of sedimentation are not additive like molecular weights are.
Before we get into the specifics of how antibiotics inhibit bacterial ribosomes, let's briefly review how ribosomes work. First, a tRNA loaded with a particular amino acid enters the ribosome at the A site. The tRNA's anticodon has to match the codon, or group of three nucleotides on the mRNA. Then, at the P site of the ribosome, a peptide bond forms between the previous amino acid and the new amino acid. Finally, the empty tRNA exits at the E site. This process repeats for the whole length of the mRNA, and the polypeptide chain continues to grow.
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Summary
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Enzyme, a substance that acts as a catalyst in living organisms, regulating the rate at which chemical reactions proceed without itself being altered in the process.
In the induced-fit theory of enzyme-substrate binding, a substrate approaches the surface of an enzyme (step 1 in box A, B, C) and causes a change in the enzyme shape that results in the correct alignment of the catalytic groups (triangles A and B; circles C and D represent substrate-binding groups on the enzyme that are essential for catalytic activity). The catalytic groups react with the substrate to form products (step 2). The products then separate from the enzyme, freeing it to repeat the sequence (step 3). Boxes D and E represent examples of molecules that are too large or too small for proper catalytic alignment. Boxes F and G demonstrate binding of an inhibitor molecule (I and I′) to an allosteric site, thereby preventing interaction of the enzyme with the substrate. Box H illustrates binding of an allosteric activator (X), a nonsubstrate molecule capable of reacting with the enzyme.
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Category: Science & Tech
Key People: Richard Henderson Emil Fischer Maud Leonora Menten Günter Blobel Arieh Warshel
Related Topics: neuraminidase renin-angiotensin system allosteric control induction cooperativity
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2. Enzymes are protein catalysts responsible
for most of the chemical reactions of the
body
They are found in: cells and all tissues;
serum to which gain access from injured
cells, cells undergone stress
3. in disease states, caused in increased
membrane permeability
caused by increase rates of
intracellular synthesis
subsequent diffusion of enzymes
Enzymes found in serum will help physicians
diagnose certain disease and aid in the
monitoring of the disease condition
4. Increase serum levels
increased release of enzyme from
source
o necrosis
o increased membrane permeability
increased size of tissue source of
enzyme
impaired excretion of enzyme
increased enzyme synthesis
6. Alkaline phosphatase – diagnose
osseous and hepatobiliary diseases
Acid phosphatase – in the diagnosis of
prostate cancers
Amylase and lipase – diagnosis of
pancreatic disease
SGPT – liver diseases (hepatitis)
SGOT – cardiac and liver diseases
7. Catalyst
A substance that enhances the rate of a
chemical reaction but is not permanently
altered by the reaction
Decreases the activation of energy required for a
chemical reaction and provides an alternative
reaction pathway that requires less energy
8. Enzymes are neither produced or
consumed in the reaction
Enzymes do not cause the reaction
but enhances the reaction to occur
Enzymes are long sequences of
amino acid
9. Enzymes are highly specific and
produce only the expected product
from given reactant or substrate
Enzymes acts on moderate pH and
temperature
10. Enzyme possess the following:
Active site – where the substrate fits
before converted to corresponding
product
Allosteric site – which binds effector
molecules or modifiers which regulates
enzyme activity
11. Apoenzyme – are protein portion of
the enzyme
Coenzyme – non-protein component;
main participant during reaction with a
substrate
12. help in enzymatic activity by orienting
properly the substrate with the active site.
Coenzyme – organic cofactor: NADH,
NADPH, FAD and FMN
Activator - usually metallic ions tightly
bound to enzymes: Mg, Zn++, Cu++
13. Other enzymes are pro-enzymes or
zymogens that are inactive but once
released to their target sites they become
activated.
Isoenzymes – enzymes with similar
enzymatic activities but differ in their
chemical structure and origins
14. They are unchanged during the
course and termination of
chemical reaction.
They demonstrate great
specificity:
Absolute – pyruvate kinase
Group - phosphatases
Bond - hydrolases
Stereospecificity - transaminases
15. Enzyme binds to a single type of
substrate because of
complementary structures of the
active site and substrate
Substrate’s overall shape and
charge allows to interact with
enzymes active site
16. Flexibility structure of protein is
taken into account
Substrate does not precisely fit
into the rigid active site instead
a non-covalent interaction of
enzyme-substrate change it
thus conforming to the shape of
active site to the shape of the
substrate
17. Substrate Concentration
Michaelis-Menten hypothesis: the rate of
substrate conversion to product is
determined by
substrate concentration and
rate of dissociation of enzyme substrate complex
first-order kinetics
At constant enzyme concentration, the velocity or speed
of the enzyme reaction initially increases as the substrate
concentration increases.
Reaction rate is dependent on the substrate
concentration
18. Zero-order kinetics
The point at which the further addition of
substrate does not anymore change the velocity
of enzyme reaction.
The reaction is now dependent on the
enzyme concentration
Km
Represents the substrate concentration where
the velocity is ½ the maximum
Represents the substrate concentration at which
the enzyme yields half the possible maximum
velocity
It is also the measure of affinity of the enzymes
with its substrate
19. Enzyme concentration
The higher the enzyme concentration the
higher is the reaction rate. (true only in
zero-order kinetics)
pH
optimal pH varies with each enzyme
20. Temperature
most denatures at 60oC
usually optimum at 37oC
there is a characteristic increase in the
reaction rate for every 10oC increase
before denaturation
21. Cofactors
metals – transition metals (Zn++. Cu++ and
Fe++) – effective electophiles
Inhibitors
Competitive (compete for active site)
Non-competitive (binds with enzyme at
place other than active site)
Uncompetitive (binds with E-S complex)
22. Enzymes expressed in units that represent
one of the following:
Increased concentration of one of the
products substrate and coenzyme
The rate of change of any 3 unit is a measure
of rate of reaction
The catalytic rate is proportional to its
concentration at normal condition
23. MICHEALIS-MENTEN HYPOTHESIS
k1 k3
E + S (ES) E + P
k2
where: k1 is rate constant for ES formation
k2 is rate constant for ES dissociation
k3 is rate constant for product
formation and release from active
site
24. International Union of Biochemistry (IUB)
Classify and name enzymes according to the type of
chemical reaction it catalyzes
Using the name of the substrate or group on which
the enzymes acts and added by suffix “-ase”
Examples:
Urease hydrolyzes urea
Amylase metabolizes starch/amylum
Phosphatase acting on phosphate esters
25. Biochemical functions, indicating
substrate, class of reaction catalyzed
designated by individual identification
numbers
For clarity, the raction is also identified
(examples are carbonic anhydrase, D-
amino acid oxidase and succinic
dehydrogenase)
26. Systemic name – nature of the reaction catalyzed
is associated with unique numercal code
designation
Of two parts: substrate(s) acted upon and a word
ending with –ase indicating the reaction involved
Example: L-Lactate:NAD+ oxidoreductase
Trivial or practical name – may be identical to the
systemic name but is often a simplification of it –
useful in everyday work
27. Example:
EC 1.1.1.27 L-Lactate:NAD+ oxidoreductase
lactate dehydrogenase
EC denotes Enzyme Commision
First number defines the class to which the enzyme
belongs
29. next two numbers indicate the subclass and sub-
subclass to which the enzyme is assigned
Example: may be differentiated from the amino
transferring subclass of the phosphate – transferring
category or the ethanol acceptor sub-class from that
accepting acyl group
The last number is the specific serial number given
to the enzyme within its subclass
30. 1. oxidoreductases - catalyzed oxidation-
reduction reactions
REDUCTION (addition of hydrogen to a double bond)
OXIDATION (removal of a hydrogen from a molecule to
leave a double bond)
The hydrogen is transferred with the use of coenzyme
L-lactate:NAD+ oxidoreductase catalyzed
pyruvate + NADH + H+ lactate + NAD+
subclasses: dehydrogenases, oxidases,
oxygenases, reductases, peroxidases, and
hydroxylases
31. 2. transferases – catalyzed reactions that
involve the transfer of groups from one
molecule to another (amine or phosphate
group)
ATP:creatine N-phosphotransferase (creatine kinase)
involves
ATP + creatine ADP + creatine phosphate
trivial names include with prefix “trans”:
transcarboxylases, transmethylases and
transaminases
32. 3. hydrolases – catalyze reactions in which
the cleavage of bonds is accomplished by
adding water
Amylase (cleavage of –C-O-C- bonds in starch)
Lipase (breaks down triglycerides to form glycerol and free
fatty acids)
Acid phosphatase and alkaline phosphatase (remove
phosphate group from a variety of molecules)
subclasses: esterases, phosphatases, peptidases
33. 4. lyases – (lysis means “splitting”)
catalyze reactions in which groups are
removed to form a double bond or are
added to a double bond (C-C, C-S, and C-N
bonds)
Aldolase (EC 4.1.2.13, D-fructose-1,6-biphosphate-D-
glyceraldehyde-3-phosphate lyase) which cleaves the 6-
carbon molecule fructose-1,6-diphosphate to produce two
3-carbon compounds: glyceraldehyde-3-phosphate and
dihydroxyacetone phosphate
subclasses: decarboxylases, hydratases, dehydratases,
deaminases, synthases
34. 5. isomerases – (heterogenous group)
catalyze several types of intramolecular
rearrangements
Where it involves in the conversion of one
isomer to another with examples of
transformation will include the change of cis
to trans; L-form to D-form; aldehyde to
ketone
the reactions are generally reversible
35. Triose phosphate isomerase (EC 5.3.1.1,
D-glyceraldehyde-3-phosphate ketol-
isomerase)
In the glycolytic pathway, involves in the
isomerization of glyceraldehyde-3-
phosphate (aldehyde) to dihydroxyacetone
phosphate (ketone)
epimerases – catalyze the inversion of
assymmetric carbon atoms
mutases – catalyze the intramolecular transfer of
functional group
36. 6. ligases – catalyze bond formation
between two substrate molecules forming a
larger molecule
Important in the activation of amino acids –
protein synthesis
Energy is always supplied by ATP
Aminoacyl-tRNA
37. 1. Substrate Measurement
This starts with a high substrate
concentration
1. Product Measurement
This starts with zero initial product level
This is more accurate
38. Endpoint analysis
the reaction is initiated by addition of substrate
and is allowed to proceed for a period of time
measurement of substrate or product is done at
the end of the reaction
Multipoint assay
this measures the change in the concentration of
the indicator substance at several intervals during
the course of the assay
39. Kinetic assay
this involves measurement of change in
concentration as a function of time
closely monitored at short interval
has advantage over the end point
if the concentration of the substrate is sufficiently
high in comparison to enzyme then rate of
reaction will be proportional to the concentration
of enzyme
thus the amount of product formed in a given
period of time would be proportional to the
amount of active enzyme present, with all other
factors remaining constant
40. Use of coupled reactions
enzymatic activity is measured by
coupling the activity with colorimetric
reaction
the colored product is measured
spectrophotometrically
41. 1. HEMOLYSIS
May cause falsely elevated enzyme concentration
1. ANTICOAGULANTS
Many anticoagulants cause adverse effects on enzyme
inhibiton, therefore, serum is preferred over plasma
1. LACTESCENT OR MILKY SERUM
May result in variable absorbance readings in
spectrophotometry
42. Enzymes are stable at 6oC for at least 24 hours and at
room temperature for lesser periods
For prolonged storage, use -20oC or lower
CK must be kept at -70oC
LD4 and LD5 – liver isoenzymes are inactivated at
refrigerator temperature