Biochemistry - Enzymes and Extremophiles Quiz
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Questions and Answers

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.</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.</p> Signup and view all the answers

    Which type of extremophile thrives in high salinity environments?

    <p>Halophiles</p> Signup and view all the answers

    What are cryophiles characterized by?

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

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

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

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

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

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

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

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

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

    What type of organism is Thermus aquaticus?

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

    At what temperature range can Thermus aquaticus survive?

    <p>50°C to 80°C</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</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.</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</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.</p> Signup and view all the answers

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

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

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

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

    In what environment was Thermus aquaticus originally discovered?

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

    What type of specificity does carboxypeptidase demonstrate?

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

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

    <p>Hexokinase</p> Signup and view all the answers

    What does linkage specificity refer to?

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

    How does temperature affect enzyme activity?

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

    Which factor does NOT affect enzyme activity?

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

    Which enzyme specifically hydrolyzes peptide bonds?

    <p>Protease</p> Signup and view all the answers

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

    <p>Stereochemical specificity</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</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</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.</p> Signup and view all the answers

    What is the primary role of enzymes in living organisms?

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

    Which statement about cofactors is true?

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

    Why are transition states important in enzyme-catalyzed reactions?

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

    What proportion of the human genome encodes enzymes?

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

    Which of the following best describes coenzymes?

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

    How do enzymes facilitate chemical reactions?

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

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

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

    What is a primary characteristic of enzymes as catalysts?

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

    What happens during the catalytic process involving enzymes?

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

    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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    Chapter 4 Enzymes PDF

    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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