Unit 3: Enzymes
MT6310 BIOCHEMISTRY LAB
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Substrate
UNIT 3: ENZYMES ● compound/s whose reaction an enzyme catalyzes
Active site
TOPIC OVERVIEW ● Specific portion of the enzyme to which a substrate
binds during reaction
A. ENZYMES
a. Enzyme Terminology Activation
b. Enzyme Catalysis ● Any process that initiates or increases the activity of
c. Classification of Enzymes an enzyme
d. Enzymes Activity
B. INHIBITORS Allosteric site
a. Types of Inhibitors ● Portion on the enzyme surface where
b. Enzyme Regulation inhibitors/activators bind to regulate catalytic
C. TRANSITION-STATE ANALOGS reactions
Inhibitor
A ENZYMES ● compound/s that slows down the rate of the reaction
Inhibition
ENZYMES ● Process that makes an active enzyme less active or
● Biological catalyst inactive
● Predominantly protein in nature with the exception of
ribozymes
Discussion Notes: (*)
● Increase the rate of reaction by 10⁹ to 10²⁰
Example
● Commonly ends with -ase
● The active site is found in the enzyme
● Blue = enzyme
● Active site = outside blue portion
○ To which the enzyme binds
Discussion Notes:
Enzymes A2 ENZYMES CATALYSIS
● Catalyst
● Biological molecule that speeds the rate of the
reaction ● Substrate-specific
● Picture: ○ Stereoselective
○ Urea is the substrate ○ Site targeting
○ Urease is the [] that will react with ● Efficient
○ Enzyme will not be altered or will no change ● Others catalyze reactions of specific types of
■ Will be used again to another reaction compounds or bonds; for example, trypsin catalyzes
hydrolysis of peptide bonds formed by the carboxyl
group of Lys and Arg
A1 ENZYME TERMINOLOGY
Discussion Notes: (*)
Breakdown of urea
Apoenzyme
● It should be urease
● Protein part of an enzyme
○ It should be specific
Trypsin can hydrolyze several peptide bonds
Cofactor
● If it is a protein, trypsin can break it down
● Non-protein position of an enzyme that is necessary for
● The urea will turn into ammonia through the
catalytic function
reaction with urease
● The first one na ma-digest sa stomach is pepsin then
Coenzyme
yung kinain natin
● Non-protein organic molecule, frequently a B vitamin,
that acts as a cofactor
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Discussion Notes:
If uncatalyzed
● You need a higher activation energy
If catalyzed
● Less activation energy will be used
Trypsin catalyzes the hydrolysis of peptide bonds formed by the
carboxy group of lysine and arginine
Discussion Notes: Mechanisms of Enzyme Catalysis
● Pag may lysine arginine it will be cut
(1) Locke-and-key model
● The enzyme is a rigid three-dimensional body
● The enzyme surface contains the active site
Discussion Notes:
● Lock-and-key model
Schematic diagram of the active site of an enzyme and the ○ Para may specific key sa door knob
participating components
(2) The Induced-fit model
Discussion Notes: ● The active site becomes modified to
accommodate the substrate
● Apoenzyme will bind first
● Para mag act upon yung enzyme sa substrate, the
coenzyme is needed
Enzyme Energetics
Discussion Notes:
● The induced-fit model
Enzymes provide an alternative pathway for reaction ○ A while ago kailangan muna ng cofactor
(a) The activation energy profile for a typical ○ But in this case, the active site of the enzyme
reaction will accommodate the substrate in itself
(b) A comparison of the activation energy profiles for
a catalyzed and uncatalyzed reactions
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SECOND SHIFTING – MARICEL RANIDO & JUNE GUEVARRA – Tues & Thurs
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7:00 AM - 10:00 AM
A3 CLASSIFICATION OF ENZYMES Discussion Notes:
● Facilitates hydrolysis reactions
1. Oxidoreductases - oxidation-reduction reactions ○ Acetylcholine forming acetate
2. Transferases - group transfer reactions ● Na breakdown siya as acetate and choline through
3. Hydrolases - hydrolysis reactions the action of acetylcholinesterase
4. Lyases - addition of 2 groups to C-C double bond, or
removal of 2 groups to create a C-C double bond 4. Lyases
5. Isomerases - isomerization reactions
6. Ligases - joining 2 molecules
1. Oxidoreductases
Discussion Notes:
Discussion Notes:
● Adds two groups to a C-C double bond
● May redox reaction na magaganap
● When we eat food, it will be digested 5. Isomerases
○ The digestion of carbohydrates starts in the
mouth wherein there is a salivary amylase
○ It will turn into a monosaccharide which is the
glucose
○ Yung mga kinain mo na pancake, pasta, will be
broken down into a small monosaccharide
○ Glucose will be broken down into a pyruvate
○ Pyruvate is an end product of the glycolysis
● Pyruvate will turn into a lactate due to the lactate
dehydrogenase enzyme Discussion Notes:
● In exercising, the pyruvate will turn into lactate
● It changes the form
2. Transferases ● Another 6-carbon molecule same silang
monosaccharide, but with the reaction of the
phosphoglucose isomerase, the glucose changes to
fructose
6. Ligases
Discussion Notes:
● Transfers a specific molecule to another one Discussion Notes:
○ Adda a specific molecule dun sa substrate
○ Aspartate amino transferase is the enzyme ● Joins two molecules, like a glue
● In real life example, pag meron ka transferase, a ● t-RNA will be helped by the synthetase to charge the
specific carbohydrate is added to the surface of the tRNA
RBC ○ It should have an amino acid na dala
parang grab
3. Hydrolases ● This should be facilitated by ATP or the energy
○ When the energy in ATP is used, it will
become AMP na
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A4 ENZYMES ACTIVITY
● Measure of how much a reaction rate is increased
● Affected by:
○ Enzyme concentration
○ Substrate concentration
○ Temperature
○ pH
○ Presence of inhibitors
Discussion Notes:
● Measure how much a reaction rate is increased
The effect of substrate concentration on the rate of an
● Affected by: enzyme-catalyzed reaction. Enzyme concentration,
○ Enzyme concentration temperature, and pH are constant
○ Substrate concentration
○ Temperature Discussion Notes:
■ Affects enzyme activity ● …
○ pH
■ Will affect the action of the
enzyme
○ Presence of inhibitors
■ Stop the reaction or slow
down the reaction
● Pag maraming substrate = maraming enzyme
○ But it doesn’t mean na madaming
enzyme, madami din product
The effect of temperature on the rate of an enzyme-catalyzed
reaction. Substrate and enzyme concentrations and pH are
constant.
Discussion Notes:
● …
The effect of enzyme concentration on the rate of an
enzyme-catalyzed reaction. Substrate concentration,
temperature, and pH are constant
Discussion Notes:
● …
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Figure 23-10. Mechanism of noncompetitive inhibition.
The inhibitor binds itself to a site other than the active
site (allosterism), thereby changing the confirmation of
the active site. The substrate still binds but there is no
catalysis
Figure 23-6. The effect of pH on the rate of an
enzyme-catalyzed reaction. Substrate and enzyme
concentrations and temperature are constant.
Discussion Notes:
● … Discussion Notes:
● ‘’
Figure 23-11. Enzyme kinetics in the presence and the
B INHIBITORS absence of inhibitors
B1 TYPE OF INHIBITORS
1. Competitive
2. Non-competitive
3. Uncompetitive
Mechanism of Action
Figure 23-9. The mechanism of competitive inhibition.
When a competitive inhibitor enters the active site, the Discussion Notes:
substrate cannot enter ● …
● Both the lock-and-key model and the induced-ft
model emphasize the shape of the active site
● However, the chemistry of the active site is the most
important
● Just 5 amino acids participate in the active site in
more than 65% of the enzymes studied to date
● These 5 are His > Cys > Asp > Arg > Glu
● 4 of these amino acids have either acidic of basic
side chains; the fifth has a sulfhydryl group (-SH)
Discussion Notes:
● …
Discussion Notes:
● … B2 ENZYME REGULATION
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Feedback control: an enzyme-regulation process where the
product of a series of enzyme-catalyzed reactions inhibits
an earlier reaction in the sequence
● The inhibition may be competitive or noncompetitive
Discussion Notes:
● …
● Figure 23.15. Effects of binding activators and
inhibitors to allosteric enzymes. The enzyme has an
Proenzyme (zymogen): an inactive form of an enzyme that equilibrium between the T form and the R form.
must have parts of its polypeptide chain hydrolyzed and
removed before it becomes active
● An example is trypsin, a digestive enzyme
● It is synthesized and stored as trypsinogen, which has
no enzyme activity
● It becomes active only after a six-amino acid fragment
is hydrolyzed and removed from the N-terminal end of
its chain
● Removal of this small fragment changes not only the
primary structure but also the tertiary structure,
allowing the molecule to achieve its active form Discussion Notes:
Discussion Notes: ● …
● …
Protein Modification: The process of affecting enzyme
Allosterism: enzyme regulation based on an event activity by covalently modifying it
occurring at a place other than the active site but that ● The best known examples of protein modification
creates a change in the active site. involve phosphorylation/dephosphorylation
● An enzyme regulated by this mechanism is called an ● Example: Pyruvate kinase (PK) is the active form of the
allosteric enzyme enzyme; it is inactivated by phosphorylation to
● Allosteric enzymes often have multiple polypeptide pyruvate kinase phosphate (PKP)
chains
● Negative modulation: Inhibition of an allosteric
enzyme
● Positive modulation: Stimulation of an allosteric
enzyme
● Regulator: A substance that binds to an allosteric
enzyme
● Figure 23.14. The allosteric effect. Binding of the
regulator to a site other than the active site changes Discussion Notes:
the shape of the active site. ● …
Isoenzyme (Isozymes): An enzyme that occurs in multiple
forms; each catalyzes the same reaction.
● Example: lactate dehydrogenase (LDH) catalyzes the
oxidation of lactate to pyruvate
● The enzyme is a tetramer of H and M chains
● H₄ is present predominantly in heart muscle
● M₄ is present predominantly in the liver and in skeletal
muscle
● FIgure 23-16 (Relative distribution of these
isoenzymes). The isozymes of lactate dehydrogenase
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(LDH). The electrophoresis gel depicts the relative
isozyme types found in different tissues
Discussion Notes:
Discussion Notes: ● …
● …
Abzyme: An antibody that has catalytic activity because it
Enzymes Used in Medicine was created using a transition state analog as an
immunogen.
(a) The molecule below is a transition analog for the
reaction of an amino acid with
pyridoxal-5’-phosphate.
(b) The abzyme is then used to catalyze the reaction on
the next screen
Discussion Notes:
● …
C TRANSITION-STATE ANALOGS
Transition state analog: a molecule whose shape mimics
the transition state of a substrate
● Figure 23.17. The proline racemase reaction and a
mimic for the transition state. Pyrrole-2-carboxylate
mimics the planar transition state of the reaction
Discussion Notes:
● …
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TABLE TITLE
KEY TERM Definition Example
KEY TERM Definition Example
B1 ABOUT THIS TEMPLATE
Additional Information
Quantification of the Enzyme Activity / Enzyme Product
1. Standardization / Control
○ Group 1 & 2
○ Preparation of test tubes: Each test
tubes will have different known
concentrations of the enzyme product
○ + Dye = to determine the different
absorbance at specific concentration
■ Then , we can plot: (double
check this part)
■ y = mx + b
■ (x) : different known
concentration
■ (y) : absorbance
■ (m) : slope of the line
■ (b) : y - intercept
2. Enzyme Product Quantification
○ Enzyme activity at varying pH and temp
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B MAIN TOPIC 2
W1: LECTURE TITLE
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E. MAIN TOPIC TITLE
a. Subtopic A1 KEY TERM Definition Example
b. Subtopic A2
B1 ABOUT THIS TEMPLATE
A MAIN TOPIC
● Originally made by kw0ndys
TECHNICAL TERM/KEY TERM ● Inspired by my own school notes and
● Definition includes design elements from Google to
● Examples (if necessary) improve its look and functionality.
Additional Information B1 REMINDERS
● Include any extra details in this section,
such as additional instructions or
insights provided by your professor, ● This template is designed exclusively for
along with any other relevant your personal use. DO NOT RESELL OR
information that may enhance your REUSE.
notes. ● This template is fully customizable.
● If you have suggestions for
improvements, please do not hesitate to
A1 WHY SCHOOL NOTES ARE ESSENTIAL let me know. Your feedback is valuable
and helps me enhance the quality of this
template.
● Making your own lecture notes helps you ● The design and content of this template
actively engage with the material, are unique to my work, and any
improves retention, and ensures the resemblance to other templates is
content is organized in a way that unintentional.
makes sense to you.
● It also allows you to personalize and
highlight key concepts, leading to more B3 HOW CAN I ACCESS THIS TEMPLATE?
effective studying and better academic
performance. ● The original copy of this template is set to
“view only” to ensure it remains
A2 ORGANIZE YOUR NOTES EFFECTIVELY unedited and intact.
5. Go to “File” at the top left corner.
● Organizing your lecture notes helps in
6. Select “Make a copy”.
creating a structured and coherent study
7. Rename your file to avoid confusion.
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● Use headings, bullet points, and
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