G11 - Bio Note - Unit 3 (Enzymes)
G11 - Bio Note - Unit 3 (Enzymes)
By: Getaneh T.
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Unit – 3
Enzymes (Enzymology)
3.1. What are enzymes?
Active
Enzymes are globular proteins which functions site
as biological catalysts, speeding up reaction
rate by lowering activation energy without
affected by the reaction being catalysed.
- Enzymes have a uniquely shaped structure or region called the active site.
Active site – the part of an enzyme molecule that binds with its substrate.
Substrate - a substance upon which an enzyme acts in a biochemical reaction.
- When a substrate bind with the active site an enzyme-substrate complex can be
formed.
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• Enzymes are proteins that act as biological catalysts (biocatalysts).
- Exception – ribozymes (RNA molecules) act as non-protein biocatalysts.
• Enzymes speed up chemical reactions by lowering the activation energy.
N.B: Activation energy (Ea) is the minimum amount of energy (free) required to
start a chemical reaction (convert reactants to products).
• Enzymes are composed of chains of amino acids linked by peptide bonds.
• All living cells contain different enzymes based on their cell type and type of
reactions taken place.
• Enzymes drive metabolism, which includes; catabolism (breakdown of molecules
and anabolism (synthesis of molecules).
Metabolism = Anabolism + Catabolism
• Metabolic processes require enzymes to catalyze reactions at life-sustaining rates.
• Enzymes act on substrates to form products, and remain unchanged after the
reaction.
Exercise 1
I. Give short answer for each of the following questions.
1. What are enzymes?
2. What are the building blocks of enzymes?
3. What is the active site of an enzyme, and how does it facilitate the enzyme's
function in catalyzing reactions?
4. What is activation energy?
5. What do we call the total amount of the biochemical reactions involved in
maintaining the living condition of the cells in an organism?
6. Distinguish between anabolism and catabolism.
7. Why are there so many different types of enzymes in your body?
8. Why is a small amount of enzyme enough for catalyzing a large number of
substrate molecules into products?
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3.2 Properties and functions of enzymes
3.2.1 General properties of an enzyme
- Enzymes are biological catalysts that accelerate reaction rates without being
consumed in the reaction.
- They do not alter the nature of products formed.
A. The physical properties of enzymes
Exercise 2
I. Give short answer for each of the following questions.
1. Describe the physical properties of enzymes.
2. Describe the chemical properties of enzymes.
3. What is denaturation in the context of enzymes and what factors can cause it?
4. What are the main factors that determine enzyme activity?
5. What type of specificity is focused on the particular substrate an enzyme can bind
and catalyze?
6. What aspect of enzyme specificity refers to the requirement for certain non-
protein molecules to assist in catalysis?
7. In the context of enzymatic reactions, what characteristic allows some enzymes
to catalyze both forward and reverse reactions?
8. How do enzymes accelerate chemical reactions?
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3.2.2 The function of enzymes
Functions of enzymes include:
- Accelerate chemical reactions in the body, acting as biological catalysts.
- Support digestion by breaking down food molecules for nutrient absorption.
- Regulate metabolism by facilitating energy production and cell processes.
- Lower activation energy of reactions, making them occur more efficiently.
- Assist in cellular functions, ensuring proper functioning of organs like the liver and
muscles.
- Act as biomarkers for diagnosing diseases such as heart attack, liver damage, and
cancer.
N.B: The turn over number (kcat) of an enzyme is the maximum number of
substrates converted to products by one enzyme molecule per second at
saturated (fully occupied) active sites.
The names of most enzymes end with the suffix “ase”. E.g. amylase.
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The breaking down of sucrose into glucose and fructose by the action of sucrase.
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Examples of enzymes
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Exercise 3
I. Write the name of an enzyme that catalyze:
1. The conversion of hydrogen peroxide into water and oxygen
2. The synthesis of ATP from ADP and inorganic phosphate (Pi)
3. The joining of DNA fragments during DNA replication and repair
4. Unwinding of DNA strands during replication and transcription
5. The phosphorylation of glucose during glycolysis
6. The breaking down of proteins at low PH
7. The hydrolysis of sucrose into glucose and fructose
8. The hydrolysis of cellulose into simple sugars
9. The removal of hydrogen atoms from a particular substrate
10. The breaking down of lipids into glycerol and fatty acids
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Exercise 4
I. For the following questions, match the letters with the appropriate description of
the graph of the energy flow of a chemical reaction shown below.
Exercise 5
I. Give short answer for each of the following questions.
1. What do we call the region on an enzyme where the substrate binds?
2. What role do enzymes play in chemical reactions?
3. How do enzymes affect reaction rates in biological systems?
4. What term describes the temporary association formed between an enzyme and
its specific substrate during a catalytic reaction?
5. What is the name of an enzyme that catalyze the hydrolysis of starch into
maltose?
6. What do we call the RNA molecules with a catalytic activity, involved in various
cellular activities?
7. What is the turnover number of an enzyme?
8. What happens to an enzyme after it catalyzes a reaction?
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3.3 Protein structures
- Protein structure is a polymer of amino acids joined by peptide bonds with three-
dimensional arrangements of atoms in amino acid chain molecules.
- The protein complex macromolecules have four structural levels:
1. The primary structure of proteins
- is he linear sequence of amino acids in a polypeptide chain, which is determined
by the genes encoding the protein.
- is stabilized by peptide bonds created between amino acids.
- Proteins with fewer than 50 amino acids are called peptides, while those with
more than 50 are polypeptides.
- Humans require 20 naturally occurring amino acids (L-α-amino acids), 11 non-
essential amino acids (synthesized in the human body), and 9 essential amino
acids (obtained from diets).
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4. The quaternary structure of proteins
- involves the assembly of two or more polypeptide chains or subunits into a
functional protein complex.
- The individual subunits (polypeptide chains) can be held together by hydrogen
bonds.
- Not all proteins have a quaternary structure; proteins such as hemoglobin (4
polypeptides) and collagen (3 polypeptides) have quaternary structures.
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Exercise 6
I. Give short answer for each of the following questions.
1. What level of protein structure involves the sequence of amino acids?
2. What determines the primary structure of a protein?
3. What type of bond stabilize the primary structure of a protein?
4. In which levels of protein structure do alpha helix and beta pleated sheet occur?
5. What type of interaction stabilize the secondary structure of proteins?
6. How do alpha helices and beta pleated sheets differ in protein structure?
7. Which level of protein structure involves the overall 3-D shape?
8. What type of interaction stabilize the quaternary structure of proteins?
9. What type of interactions stabilize the tertiary structure of a protein?
10. How do quaternary structures differ from tertiary structures in proteins?
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2. Induced fit model of enzyme action (Koshland, 1958)
• states that the enzyme's active site is flexible and undergoes a conformational change
to fit the substrate upon binding.
• The binding of the substrate induces changes in the enzyme’s shape, optimizing the fit
for catalysis.
• When the substrate binds, it induces a structural change in the enzyme, forming an
enzyme-substrate complex, which lowers the activation energy of the reaction and
increase the reaction rate.
• The induced fit enhances or suppresses enzyme activity by stabilizing the transition
state.
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Exercise 7
I. Give short answer for each of the following questions.
1. What is the fundamental concept behind the lock-and-key model of enzyme
binding?
2. How does induced fit model differ from the lock-and-key model in terms of
enzyme-substrate interactions?
3. What role does the active site play in enzyme binding models?
4. Which enzyme binding model suggests a rigid, pre-existing active site for
substrate binding?
5. In the induced fit model, what happens to the enzyme’s active site upon
substrate binding?
6. Which enzyme binding model better accommodates the idea of dynamic changes
in an enzyme molecule upon binding to a substrate?
7. What is enzymatic transition state?
8. How does an enzyme influence the transition state of a chemical reaction?
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1. Allosteric enzymes
- are enzymes that have additional binding sites called allosteric sites (or regulatory
sites) apart from the active site.
- active site - where the substrate binds.
- allosteric site (non-active site) - where effectors (activators or inhibitors) bind.
- Effectors (activators or inhibitors) bind reversibly to the allosteric site, causing
conformational changes in the enzyme's active site and modulating its catalytic
activity.
- activators – increase the catalytic activity of enzymes.
- inhibitors – decrease the catalytic activity of enzymes.
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Activation by phosphorylation and dephosphorylation
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Exercise 8
I. Give short answer for each of the following questions.
1. What is the primary purpose of enzyme regulation?
2. What are regulatory enzymes?
3. Distinguish between allosteric enzymes and covalently modulated enzymes.
4. What are the binding sites of substrates and effectors in allosteric enzymes,
respectively?
5. What is phosphorylation and what is its significance in enzyme regulation?
6. How does genetic modification and covalent modification of enzymes vary?
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3. Enzyme inhibition
- Enzyme inhibition is the process of decreasing or stopping the catalytic activity of
an enzyme by enzyme inhibitors.
- There are two types of enzyme inhibition.
a. Irreversible inhibitor - permanently blocks the action of an enzyme through
covalent strong irreversible interactions.
b. Reversible inhibitor - inactivates an enzyme temporarily through non-covalent
easily reversed interactions.
- Reversible inhibitors can be competitive, non-competitive or uncompetitive.
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4. Feedback (end product) inhibition
- is a type of negative feedback that can be used to control metabolic pathways.
- In feedback inhibition, the end product binds to the allosteric site of the enzyme
and change the structure of the active site of an enzyme.
- Due to feedback inhibition, a cell is able to know whether the amount of a product
is enough for its subsistence or not.
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Exercise 9
I. Give short answer for each of the following questions.
1. What is the difference between inhibitors and activators?
2. How does competitive inhibition affect enzyme activity?
3. How does reversible inhibition differs from irreversible inhibition?
4. What is the role of feedback inhibition in cellular processes?
5. How does uncompetitive inhibition alter the rate of enzymatic reactions?
6. How does non-competitive inhibition affect enzyme activity?
7. Describe some applications of inhibitors.
8. How does enzyme inhibition contribute to the treatment of diseases like
HIV/AIDS?
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3.6 Types of enzymes
3.6.1 Enzyme structural classification
• Enzymes are classified into two categories based on their structure;
1. Simple enzymes - comprise only proteins (amino acid chains), active without
additional components.
2. Conjugated enzymes (holoenzymes) - composed of both protein and non-protein
components.
a. Protein part (apoenzyme) - inactive on its own. -
- requires the non-protein part to function.
b. Non-Protein part (cofactor) - essential for enzyme activity.
- Cofactors can be coenzymes or mineral (metal) ions.
i. Coenzymes - organic molecules necessary for the catalytic activity of enzymes.
- most are derived from vitamins and often bound loosely to an apoenzyme.
- E.g. NAD (derived from niacin (B3), and FAD (derived from riboflavin (B2).
ii. Mineral (metal) ions – inorganic molecules necessary for the catalytic activity of
enzymes.
- usually bound tightly to an apoenzyme
- E.g. Mg 2+, Fe2+, Zn2+, Mn+, Cu2+, etc…
N.B: Cofactors that bound very tightly to apoenzyme are called prosthetic groups. 41
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Exercise 10
I. Give short answer for each of the following questions.
1. Define the following biological terms.
a. Holoenzyme d. Apoenzyme
b. Coenzyme e. Prosthetic group
c. Simple enzymes f. Isoenzymes
2. What is the function of a metal ion in enzyme catalysis?
3. Give examples of inorganic cofactors.
4. Give examples of coenzymes.
5. Why is the presence of a cofactor critical for some enzymes?
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3.6.2 Basic classification of enzymes
- Based on the type of reactions that they catalyze, enzymes are classified into six
functional classes.
- The followings are the six basic classes of enzymes.
1. Oxidoreductases - catalyzes redox reactions.
- It catalyzes the transfer of electrons from one molecule (reductant) to the other
molecule (oxidant).
- Rxn example: A– + B → A + B, where A is the reductant (electron donor) and
B is the oxidant (electron acceptor).
- Examples of oxidoreductases include; hydroxylases, oxygenases…
2. Transferases - catalyze the transfer of functional groups like methyl and
phosphate from one donor molecule to acceptor molecule.
А-В + С → А + В-С
- Examples of transferases include; transaminases, kinases…
3. Hydrolases - catalyze the hydrolysis of chemical bonds.
А-В + Н2О → А-Н + В-ОН
- Examples of hydrolases include; digestive enzymes, esterase's…
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The scientific name of amylase is EC 3.2. 1.1.
Class sub-class sub-sub class serial number (specific name)
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Exercise 11
I. Give short answer for each of the following questions.
1. Which class of enzyme is responsible for catalyzing the transfer of electrons in
redox reactions?
2. Which class of enzymes is involved in transferring functional groups between
molecules?
3. Which enzyme class is crucial for breaking down large molecules into smaller
ones through hydrolysis?
4. Which enzyme class is associated with the formation of new bonds between
molecules using ATP?
5. Which enzyme class participates in the rearrangement of atoms within a
molecule?
6. Which enzyme class is associated with the formation or cleavage of bonds
between molecules without hydrolysis or oxidation?
7. To which class of enzymes do digestive enzymes such as pepsin and amylase
belong?
8. Distinguish between endoenzymes (intracellular) and exoenzymes (extracellular)
with examples.
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Question: Explain how each of the above factors affect enzymes’ activity. 48
3.7.1 Description of factors affecting enzymatic action
1. Temperature
- Optimum temperature – specific ranges of temperature at which enzymes work
best (effectively and efficiently).
- Low temperatures – slow down enzyme activity by reducing kinetic energy, leading
to fewer enzyme-substrate collisions.
- Extreme high temperatures – denature enzymes, altering their structure and
causing loss of activity.
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3. Substrate concentration s
- Increasing s increases the reaction rate by increasing collisions between enzymes
and substrates resulting in the formation of more ES complex.
- Once all enzyme active sites are occupied and saturated with substrate, the
reaction rate reaches its maximum (plateau).
- Further increases in substrate concentration do not affect the reaction rate.
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Exercise 12
I. Give short answer for each of the following questions.
1. What are extremozymes? Provide examples of organisms that produce them.
2. What are proenzymes (zymogens), and provide examples?
3. What do we call the temperature at which enzymes work best?
4. How does too high temperature affect enzyme activity?
5. Which enzyme in the human body works best in too acidic (low pH) conditions?
6. What happens to the reaction rate when enzyme concentration increases with
abundant substrate?
7. Why does the reaction rate plateau (become constant) at high substrate
concentrations?
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Exercise 13
I. Give short answer for each of the following questions.
1. Define enzyme kinetics.
2. Which factors influence the rate of enzyme-catalyzed reactions in enzyme
kinetics?
3. Explain the Michaelis-Menten model of enzyme kinetics.
4. Write the Michaelis-Menten equation.
5. In the Michaelis-Menten equation, what does Vmax represent and what is its role
in describing enzymatic reactions?
6. What do we call the substrate concentration required to achieve half of the
maximum reaction rate (Vmax)?
7. What are the implications of low and high Km values for an enzyme's interaction
with its substrate?
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Exercise 14
I. Give short answer for each of the following questions.
1. What types of enzymes are used in detergents, and what do they do?
2. What enzymes are used in the leather industry, and what is their purpose?
3. Define malting and describe its main steps.
4. Which type of grain is most commonly used for malting?
5. What is biochemistry, and what are its main areas of study?
6. Describe the application of each of the following enzymes.
a. Pectinase in food industry
b. Beta-glucanase brewing industry
c. Papain in food industry
d. Arginase in medical industry
e. Proteases in tannery industry
f. Lipase in tannery industry
g. Alpha- and beta-amylases in malting
h. Lactase in dairy industry
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Thank You!
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