Biochemistry - Enzymes and Extremophiles Quiz
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What is the turnover number of an enzyme?

  • The ratio of substrate to enzyme in a reaction.
  • The rate at which enzyme concentration decreases over time.
  • The total number of enzymes present in a reaction mixture.
  • The number of substrate molecules transformed per minute by one enzyme molecule under optimum conditions. (correct)

    • Why do cells maintain a lower concentration of enzymes compared to substrates?

  • It prevents substrate from becoming saturated too quickly.
  • It allows for faster reactions without energy costs. (correct)
  • It helps synchronize cellular metabolic processes.
  • Enzymes are used up in reactions, requiring constant synthesis.

    • Which of the following best describes an extremophile?

  • An organism that survives only in conditions typical for human life.
  • A microorganism that thrives in extreme environments unsuitable for most life forms. (correct)
  • A microorganism that thrives in a wide range of environmental conditions.
  • A species that requires minimal environmental adaptation.

    • What are extremozymes?

    <p>Microbial enzymes that work effectively under extreme conditions. (B)</p> Signup and view all the answers

    What is one characteristic of extremozymes that makes them useful in industrial processes?

    <p>They can tolerate extreme temperatures and pressures. (A)</p> Signup and view all the answers

    Which type of extremophile thrives in high salinity environments?

    <p>Halophiles (C)</p> Signup and view all the answers

    What are cryophiles characterized by?

    <p>Optimal growth at temperatures of 15°C or lower. (A)</p> Signup and view all the answers

    What pH condition is optimal for the enzymatic activity of pepsin?

    <p>pH 2.0 (B)</p> Signup and view all the answers

    What is the consequence of protonation or deprotonation of groups on the substrate at pH levels outside the enzyme's optimum?

    <p>Reduced enzymatic activity (A)</p> Signup and view all the answers

    What notable adaptation occurs in bacteria within the acidic environment of the human stomach?

    <p>Ability to proliferate in low pH (C)</p> Signup and view all the answers

    What was the initial belief regarding the cause of stomach ulcers before the discovery of H. pylori?

    <p>Excess stomach acid (A)</p> Signup and view all the answers

    Who conducted self-experimentation to prove the link between H. pylori and gastritis?

    <p>Barry Marshall (B)</p> Signup and view all the answers

    What occurred when Marshall drank a culture of H. pylori?

    <p>He developed gastritis (D)</p> Signup and view all the answers

    What did Marshall and Warren receive the Nobel Prize for in 2005?

    <p>Discovery of Helicobacter pylori (B)</p> Signup and view all the answers

    What type of organism is Thermus aquaticus?

    <p>A rod-shaped bacterium (B)</p> Signup and view all the answers

    What was one of the effects observed in Marshall’s gastric secretions after consuming H. pylori?

    <p>Absence of hydrochloric acid (C)</p> Signup and view all the answers

    At what temperature range can Thermus aquaticus survive?

    <p>50°C to 80°C (A)</p> Signup and view all the answers

    What impact does low (2.0) pH have on enzymes like pepsin and trypsin?

    <p>Maintains their tertiary structure (B)</p> Signup and view all the answers

    What characteristic of Thermus aquaticus enzymes contributes to their stability at high temperatures?

    <p>They are held together by more attractive forces. (D)</p> Signup and view all the answers

    What was a significant observation made by J. Robin Warren about ulcer patients?

    <p>Increased bacteria correlated with inflammation (A)</p> Signup and view all the answers

    Why is the discovery of Thermus aquaticus considered important?

    <p>It contributes to the advancement of PCR techniques. (C)</p> Signup and view all the answers

    What is Polymerase Chain Reaction (PCR) primarily used for?

    <p>Amplifying specific segments of DNA. (B)</p> Signup and view all the answers

    How does Thermus aquaticus's enzyme structure compare to those that function at lower temperatures?

    <p>It has more attractive forces. (C)</p> Signup and view all the answers

    What might happen to enzymes if the temperature exceeds 80°C?

    <p>They become inactive. (D)</p> Signup and view all the answers

    In what environment was Thermus aquaticus originally discovered?

    <p>A hot spring (B)</p> Signup and view all the answers

    What type of specificity does carboxypeptidase demonstrate?

    <p>Group specificity (D)</p> Signup and view all the answers

    Which enzyme catalyzes the addition of a phosphoryl group to glucose?

    <p>Hexokinase (D)</p> Signup and view all the answers

    What does linkage specificity refer to?

    <p>Action on a particular type of bond (D)</p> Signup and view all the answers

    How does temperature affect enzyme activity?

    <p>It increases enzyme denaturation at high levels (D)</p> Signup and view all the answers

    Which factor does NOT affect enzyme activity?

    <p>Volume of reaction mixture (C)</p> Signup and view all the answers

    Which enzyme specifically hydrolyzes peptide bonds?

    <p>Protease (B)</p> Signup and view all the answers

    Which type of specificity ensures an enzyme acts on specific stereoisomers of compounds?

    <p>Stereochemical specificity (D)</p> Signup and view all the answers

    What effect does increased temperature have on enzyme activity, up to a certain point?

    <p>It increases the number of substrate-enzyme collisions (C)</p> Signup and view all the answers

    L-amino acid oxidase can only catalyze the oxidation of which form of amino acids?

    <p>L-form (D)</p> Signup and view all the answers

    Which of the following statements about the specificity of enzymes is false?

    <p>Enzyme specificity is irrelevant to their function. (C)</p> Signup and view all the answers

    What is the primary role of enzymes in living organisms?

    <p>To catalyze metabolic reactions (A)</p> Signup and view all the answers

    Which statement about cofactors is true?

    <p>Cofactors provide additional reactive functional groups (B)</p> Signup and view all the answers

    Why are transition states important in enzyme-catalyzed reactions?

    <p>They determine the rate of the reaction (D)</p> Signup and view all the answers

    What proportion of the human genome encodes enzymes?

    <p>Approximately 25% (B)</p> Signup and view all the answers

    Which of the following best describes coenzymes?

    <p>They are complex organic or metalloorganic molecules (D)</p> Signup and view all the answers

    How do enzymes facilitate chemical reactions?

    <p>By stabilizing transition states (C)</p> Signup and view all the answers

    What is necessary for dietary metal ions to be effective as cofactors?

    <p>They must come from food (C)</p> Signup and view all the answers

    Which vitamins are most often involved in the synthesis of coenzymes?

    <p>B vitamins (A)</p> Signup and view all the answers

    What is a primary characteristic of enzymes as catalysts?

    <p>They remain unchanged after the reaction (B)</p> Signup and view all the answers

    What happens during the catalytic process involving enzymes?

    <p>Substrates are converted into products (B)</p> Signup and view all the answers

    Flashcards

    Thermus aquaticus

    A rod-shaped bacterium that thrives in extremely hot environments like hot springs.

    Polymerase Chain Reaction (PCR)

    A laboratory technique used to rapidly amplify specific DNA sequences.

    Enzyme Turnover Number

    The number of substrate molecules transformed per minute by one enzyme molecule under optimal conditions.

    DNA amplification

    A process that increases the number of copies of a specific DNA segment.

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    Extremophile

    A microorganism that thrives in extreme environments, like very high temperatures or pressures.

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    Enzymes

    Biological catalysts that speed up chemical reactions in living organisms.

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    Extremozymes

    Enzymes found in extremophiles, which can function in conditions that would inactivate enzymes from most other organisms.

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    Hyperthermophiles

    Organisms that thrive in high temperatures and pressures, such as deep-sea vents.

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    Thermostability

    The ability of an organism to survive and function at high temperatures.

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    Halophiles

    Organisms that thrive in environments with high salt concentrations.

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    Attractive forces

    The attractive forces that hold molecules together, affecting their stability and function.

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    Enzyme stability

    The process by which enzymes maintain their structure and function at high temperatures.

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    Xerophiles

    Organisms that thrive in extremely dry conditions.

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    Cryophiles

    Organisms that thrive in very cold temperatures.

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    Temperature tolerance

    The temperature range at which an organism can survive and function.

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    Group Specificity

    The enzyme will only act on molecules with a specific functional group, such as hydroxyl, amino, or phosphate.

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    Linkage Specificity

    The enzyme will act on a particular type of chemical bond, regardless of the rest of the molecule's structure.

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    Stereochemical Specificity

    The enzyme will only act on a specific stereoisomer, like a left or right hand.

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    Enzyme Activity

    The rate at which an enzyme converts a substrate into a product.

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    Temperature and Enzyme Activity

    Higher temperatures lead to faster molecule movement, increasing collisions between enzymes and substrates.

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    pH and Enzyme Activity

    Each enzyme has an optimal pH at which it functions best.

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    Substrate Concentration and Enzyme Activity

    Increasing substrate concentration increases enzyme activity until saturation is reached.

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    Enzyme Concentration and Enzyme Activity

    Higher enzyme concentration leads to faster reaction rates.

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    Enzyme Denaturation

    An enzyme's structure can be irreversibly changed at high temperatures, leading to loss of function.

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    Enzyme-Substrate Complex

    The enzyme-substrate complex is a temporary association formed when the enzyme binds to its specific substrate.

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    What are enzymes?

    Special proteins (or sometimes RNA) that accelerate chemical reactions within living cells.

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    What kinds of reactions do enzymes catalyze?

    Metabolic reactions within cells, like breaking down food for energy or building complex molecules.

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    Why are enzymes important for life?

    Enzymes are crucial because they speed up reactions that would otherwise occur very slowly, allowing life to function.

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    How do enzymes work?

    Enzymes bind to specific molecules called substrates, bringing them into the right position to react.

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    What is a transition state?

    The highest-energy state in a chemical reaction pathway. Enzymes stabilize this state, accelerating the reaction.

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    Do all enzymes work alone?

    Some enzymes require no additional components for activity, while others need cofactors like inorganic ions or organic molecules.

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    What are inorganic cofactors?

    Inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+, that help enzymes function.

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    What are coenzymes?

    Complex organic molecules that assist enzymes. They often contain vitamins or vitamin derivatives.

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    What is an apoenzyme?

    The protein part of an enzyme that requires a cofactor to be active.

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    Why do apoenzymes need cofactors?

    Coenzymes provide additional functional groups needed for enzyme activity, expanding their capabilities.

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    Pepsin's optimal pH

    Pepsin functions best at a low pH (about 2.0) because its amino acid sequence allows it to maintain its tertiary structure in acidic environments.

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    Trypsin's optimal pH

    Trypsin functions best at a higher pH (about 8.0) because its amino acid sequence allows it to maintain its tertiary structure in less acidic environments.

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    Enzyme Structure & pH

    The tertiary structure of an enzyme is crucial for its activity. Changes in pH can affect the enzyme's shape and ability to bind with substrates.

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    Pickling and Microorganisms

    Pickling, a process of preserving food in vinegar, creates a very acidic environment (low pH) that inhibits the growth of harmful microorganisms.

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    H. pylori and Stomach Ulcers

    H. pylori bacteria are a common cause of stomach ulcers, a condition previously attributed to factors like stress and spicy food.

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    H. pylori's Adaptation

    H. pylori thrive in the acidic environment of the stomach, adapting to survive in a way that's not typical for most bacteria.

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    Warren's Observation

    J. Robin Warren, a clinical pathologist, noticed a correlation between the severity of stomach inflammation and the presence of H. pylori bacteria.

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    Marshall's Experiment

    To confirm the role of H. pylori in gastritis, Barry Marshall drank a culture of the bacteria and observed the development of symptoms.

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    Koch's Postulates

    Koch's postulates are a set of criteria used to determine if a microorganism is the cause of a disease.

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    Nobel Prize for H. pylori Discovery

    Marshall and Warren's discovery of H. pylori's role in gastritis and ulcers earned them the Nobel Prize in Medicine in 2005.

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    Study Notes

    Chapter 4: Enzymes

    • Enzymes are highly effective catalysts for chemical reactions due to their ability to specifically bind a wide range of molecules.
    • They precisely orient substrates to optimize chemical bond breaking and formation.
    • Enzymes stabilize transition states, the highest-energy species in reaction pathways.
    • By doing so, they determine which reaction pathways will proceed.

    Introduction

    • Thermus aquaticus, a rod-shaped bacterium, thrives in hot springs of Yellowstone National Park.
    • It survives at temperatures between 50°C and 80°C.
    • This bacterium's enzyme function is stable even above water's boiling point.
    • The discovery of T. aquaticus is important for Polymerase Chain Reaction (PCR).

    Introduction - Why was its discovery important?

    • Polymerase Chain Reaction (PCR) is a laboratory technique used to quickly produce millions to billions of copies of a specific DNA segment.
    • PCR steps include denaturation (94-96°C), annealing (68°C), and elongation (72°C).
    • Taq polymerase, an enzyme from T. aquaticus, is stable at high temperatures required in PCR, enabling the amplification of DNA sequences.

    Introduction - Biological Catalysis

    • Biological catalysis was first noted in the late 1700s via studies on meat digestion by stomach secretions.
    • 1800s research focused on starch to sugar conversion.
    • In 1850s, Louis Pasteur identified "ferments" as inseparable from live yeast cells, a concept known as vitalism, which dominated up to 1897.
    • Eduard Buchner's 1897 discovery of yeast extracts capable of fermentation without live yeast disproved vitalism.

    Introduction

    • Frederick W. Kühne coined the term "enzymes" for molecules detected by Buchner.
    • James Sumner's 1926 isolation and crystallization of urease marked a breakthrough in early enzyme studies.
    • John Northrop and Moses Kunitz later crystallized pepsin, trypsin, and other digestive enzymes; confirming they were also proteins.
    • J.B.S. Haldane, during this time period, wrote a treatise titled Enzymes, suggesting weak bonding interaction between enzymes and substrates are used to catalyze reactions.

    Introduction - Enzymes: The Catalysts of Life

    • Living organisms have thousands of chemical reactions continuously occurring within their cells.

    • Enzymes, primarily proteins (occasionally RNA), catalyze all metabolic reactions.

    • They break down food molecules for energy and participate in biosynthetic reactions to create biomolecules.

    • About a quarter of human genes encode enzymes.

    • Enzymes are highly specific, binding to particular molecules called substrates.

    • They bring substrates together in an optimal orientation for chemical reactions.

    • They catalyze reactions by stabilizing transition states, which are the highest-energy species in reaction pathways.

    Enzymes - Cofactors and Coenzymes

    • Some enzymes need no additional components, whereas others require cofactors (inorganic ions) or coenzymes (organic molecules), both of which are essential for enzymatic activity. Some examples of cofactors are Fe2+, Mg2+, Mn2+, and Zn2+.
    • Coenzymes act as transient carriers of atoms or functional groups facilitating their transfer between substances. The structures and roles of various coenzymes (like Biocytin, Coenzyme A etc are described in detail.)
    • Metal ions, necessary cofactors, are supplied through dietary intakes. Coenzymes are synthesized within the body using components obtained from other nutrients.

    Enzymes - Holoenzymes, Apoenzymes, and Prosthetic Groups

    • A complete, catalytically active enzyme, including its bound cofactor (and/or metal ions), is called a holoenzyme.
    • The protein part of a holoenzyme (without the cofactor) is called the apoenzyme (or apoprotein).
    • A tightly or even covalently bound coenzyme that's part of an enzyme is a prosthetic group.

    Enzyme Catalysts

    • Enzymes are highly effective catalysts in biological systems due to their ability to lower activation energy required for the reaction to proceed.
    • The presence of an enzyme reduces the free energy of activation required for a reaction to occur, but it does not alter the free energy difference between the products and reactants.

    Enzyme Nomenclature and Classification

    • The three main aspects in enzyme nomenclature are the suffix '-ase' indicating a substance is an enzyme, the reaction type, and the substrate.
    • Enzyme classes are categorized by the types of reactions they catalyze (oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases).
    • Examples of enzymes include cellulase, sucrase, L-amino acid oxidase, and aspartate aminotransferase.

    Enzyme Nomenclature and Classification - Oxidoreductases

    • Oxidoreductases catalyze oxidation-reduction reactions.
    • Oxidation increases the number of C-O bonds and decreases the number of C-H bonds.
    • Reduction decreases the number of C-O bonds and increases the number of C-H bonds.
    • In these reactions, oxidation and reduction occur together. Example: Lactate dehydrogenase.

    Phenolase and Enzymatic Browning

    • Phenolase is the enzyme that causes enzymatic browning of fruits and vegetables.
    • Substrates such as phenol derivatives can be oxidized to a-benzoquinone derivatives by phenolase.
    • This reaction can be prevented or slowed by minimizing oxygen exposure and reducing enzyme activity through temperature control.
    • Ascorbic acid can function as an antioxidant to prevent browning.

    Proteome Complexity

    • Enzyme proteins can be modified covalently by processes like phosphorylation and glycosylation, and these modifications are often involved in their regulation.

    Enzyme Quick Quizzes

    • Conjunction enzymes have non-protein portions.
    • Metal Ions and coenzymes are cofactors.
    • Cofactors may or may not be covalently bound to apoenzymes.

    Gibbs Free Energy

    • Gibbs Free Energy (G) is a thermodynamic property that measures the energy available to do useful work in a reaction.
    • For a spontaneous reaction, ΔG is negative; for a reaction at equilibrium, ΔG is zero. For a nonspontaneous reaction, ΔG is positive.
    • Factors like the free energy difference between products and reactants (ΔG) and the energy needed to initiate the reaction (Energy of activation, Ea) are crucial for understanding enzyme function.

    Enzyme Action - How Enzymes Speed Up Reactions

    • Enzymes speed up reactions by lowering the activation energy.
    • Enzymes create different reaction pathway.
    • The energy difference between reactants and products is not changed.

    Enzyme Action - Transition State

    • A transition state is an unstable intermediate form of substrate in the middle of a reaction.
    • Enzymes stabilize the transition state.
    • Enzymes can alter the reaction rate but do not alter the reaction equilibrium.

    Enzyme Action - Evidence for Enzyme-Substrate Complexes

    • At constant enzyme concentrations, the reaction rate increases as the substrate concentration increases.
    • Spectroscopic characteristics of enzymes and substrates may change in the presence of each other (enzyme-substrate complexes).

    Enzyme Action - Properties of Active Sites

    • Active sites are usually three-dimensional clefts or crevices.
    • Active sites are formed from groups from different amino acid sequence and residues.
    • Active sites are small volumes compared to overall enzyme volume.
    • Active sites are unique microenvironments and exclude water unless it's a reactant.

    Enzyme Action - Subtrate Binding

    • Substrates bind to enzymes through multiple weak interactions (electrostatic interactions, hydrogen bonds, and van der Waals forces).

    Enzyme Action - Specificity of Enzyme-Substrate Binding

    • Enzymes have specificities to particular substrates.
    • The "lock-and-key model" describes the precise fit between an enzyme's active site and its substrate.
    • The "induced-fit model" describes how the active site molds to the substrate.
    • The presence of binding energy is vital in lowering activation energy.

    Enzyme Activity - Factors Affecting Activity

    • Temperature affects enzyme activity. Increasing temperature initially increases enzyme activity to an optimal temperature then drops off as heat denatures the enzyme.
    • pH affects enzyme activity based on the optimal pH for each enzyme.
    • Substrate concentration increases the rate until the maximum reaction rate is reached and the concentration becomes constant with no further impact on reaction rate.
    • Enzyme concentration increasing enzyme concentration increase the reaction rate as more available active sites to accommodate the substrate are available.

    Extremophiles and Extremozymes

    • Extremophiles are organisms that live in extreme environments (high temperature, high salt, high pressure, acidity, extreme dryness).
    • Extremozymes are enzymes from extremophiles providing solutions to a wide range of industrial applications, including laundry detergents.
    • Studying extremophiles and extremozymes reveals enzyme activities that operate under varied conditions, offering new avenues for enzyme discovery.

    Regulation of Enzyme Activity - Feedback Control

    • Feedback control maintains metabolic homeostasis by regulating enzyme activity to avoid substrate or product waste.
    • Feedback regulation often uses allosteric enzymes, protein activation or inactivation, and covalent modification to regulate cellular function.

    Regulation of Enzyme Activity - Proteolytic Enzymes and Zymogens

    • Proenzymes or zymogens are inactive enzyme forms that turn active at specific sites to control enzyme functions in cell.
    • Proteolytic enzymes are enzymes that turn inactive proenzymes to active enzymes by cleaving peptide segments.

    Regulation of Enzyme Activity - Covalent Modification

    • Covalent modification is a common method of enzyme regulation.
    • Phosphorylation (adding phosphate group) or dephosphorylation (removing phosphate group) of specific amino acids within an enzyme causes changes in activity.
    • Often, phosphorylation activates the enzyme, but not always.

    Enzyme Inhibition - Types

    • Enzyme inhibitors are molecules that limit or nullify an enzyme's activity.
    • Irreversible inhibitors form strong covalent bonds with the enzyme, whereas reversible inhibitors form weaker, non-covalent bonds.
    • Competitive inhibitors resemble the substrate, competing for the active site (reversible).
    • Noncompetitive inhibitors bind to an enzyme site different from the active site (reversible).

    Enzyme Inhibition - Details

    • Irreversible inhibitors permanently disrupt enzyme activity.
    • Reversible, competitive inhibitors reduce enzyme activity but not permanently, often competing with substrates for the active enzyme site.
    • Reversible, noncompetitive inhibitors bind at a site other than the active site, preventing substrate binding regardless of substrate concentration.
    • Specific examples of inhibitors include arsenic, penicillin, and certain heavy metals (Hg2+, Pb2+, and Ag+).

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    Description

    Test your knowledge on enzymes and extremophiles with this quiz. Discover key characteristics of extremozymes and how specific extremophiles thrive in extreme conditions. This quiz is perfect for students interested in biochemistry and microbiology.

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