Biology: Enzymes and Protein Structure
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Questions and Answers

What can happen to an enzyme at suboptimal temperatures?

  • The enzyme increases its substrate binding affinity.
  • The enzyme becomes more efficient.
  • The enzyme maintains its shape.
  • The enzyme can denature and lose its shape. (correct)

What occurs when a substrate binds to the active site of an enzyme?

  • The substrate forms permanent bonds with the enzyme.
  • The enzyme is destroyed by the substrate.
  • The substrate becomes inactivated.
  • Temporary bonds are formed, weakening original substrate bonds. (correct)

What is the function of the enzyme-substrate complex?

  • It breaks down the substrate into amino acids.
  • It allows new bonds to form between substrates. (correct)
  • It creates permanent bonds between enzyme and substrate.
  • It increases the activation energy required for the reaction.

What is activation energy?

<p>The energy required for reactants to engage in a reaction. (C)</p> Signup and view all the answers

What role do catalysts play in biochemical reactions?

<p>They enable reactions to occur at lower activation energies. (B)</p> Signup and view all the answers

What happens to the enzyme-substrate complex after the reaction?

<p>It breaks apart to yield the products of the reaction. (B)</p> Signup and view all the answers

Which factor does NOT affect enzyme function?

<p>Substrate shape (A)</p> Signup and view all the answers

What must happen to the energy from exergonic reactions for it to be used in endergonic reactions?

<p>It must be directly transferred to ATP. (C)</p> Signup and view all the answers

Which of the following best describes ATP's role in cells?

<p>It is the universal energy carrier. (C)</p> Signup and view all the answers

What is the outcome when ATP is broken down?

<p>It transforms into ADP and phosphate. (D)</p> Signup and view all the answers

Which statement correctly describes oxidation and reduction?

<p>Oxidation is the loss of electrons, and reduction is the gain of electrons. (A)</p> Signup and view all the answers

What does the acronym OIL RIG stand for?

<p>Oxidation Is Loss, Reduction Is Gain. (B)</p> Signup and view all the answers

In oxidation-reduction reactions, what role does a reducing agent play?

<p>It facilitates the reduction of another substance by being oxidized. (B)</p> Signup and view all the answers

Why is oxygen considered a strong oxidizing agent?

<p>It effectively accepts electrons. (D)</p> Signup and view all the answers

What is the unstable state called when reactants become contorted and able to break or make bonds?

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

What happens during endergonic reactions?

<p>Energy is consumed to form products. (B)</p> Signup and view all the answers

How do enzymes help substrates reach their transition state?

<p>By providing an optimal environment within the active site (C)</p> Signup and view all the answers

Which of the following factors does NOT alter enzyme activity?

<p>Color of the enzyme (C)</p> Signup and view all the answers

Which enzyme is specifically responsible for adding phosphate groups?

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

What effect does increasing temperature have on enzyme activity?

<p>Increases kinetic energy and collision frequency (D)</p> Signup and view all the answers

What suffix do all enzymes end with, indicating their functional role?

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

Which statement about the activation energy of a catalyzed reaction is true?

<p>Activation energy decreases. (A)</p> Signup and view all the answers

What best describes the role of cofactors and coenzymes in enzyme activity?

<p>They can affect enzyme activity positively or negatively. (B)</p> Signup and view all the answers

What drives a reversible chemical reaction according to the law of mass action?

<p>The concentration of products and substrates (D)</p> Signup and view all the answers

What results from the phenomenon of end product inhibition?

<p>A decrease in the enzymatic activity at branch points (A)</p> Signup and view all the answers

Which of the following best describes branched metabolic pathways?

<p>They can lead to multiple products from the same substrate (D)</p> Signup and view all the answers

What is a primary function of enzymes in biological reactions?

<p>Lower the activation energy of the reaction (D)</p> Signup and view all the answers

How does allosteric inhibition function within a metabolic pathway?

<p>It prevents the substrate from binding at the active site (C)</p> Signup and view all the answers

What occurs as a result of an inborn error of metabolism?

<p>Deficiency of a specific enzyme in the pathway (C)</p> Signup and view all the answers

Which model describes the initial interaction between an enzyme and its substrate?

<p>Lock-and-key model (B)</p> Signup and view all the answers

According to the first law of thermodynamics, what is true about energy?

<p>Energy can be transformed but not destroyed (A)</p> Signup and view all the answers

How do enzymes facilitate reactions without being consumed?

<p>They are not changed by the reaction (D)</p> Signup and view all the answers

What determines the specific function of an enzyme?

<p>The enzyme's 3D shape (B)</p> Signup and view all the answers

What is the role of carbonic anhydrase in the body?

<p>To facilitate the reversible reaction between carbon dioxide and water (B)</p> Signup and view all the answers

What are the reactants called that enzymes act upon?

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

What is the purpose of negative feedback at branch points in metabolic pathways?

<p>To regulate the flow and balance of metabolic products (A)</p> Signup and view all the answers

Which statement about enzymes is true?

<p>Enzymes do not affect the nature of the reaction (C)</p> Signup and view all the answers

What occurs during the induced-fit model of enzyme activity?

<p>The enzyme changes shape to better fit the substrate after initial binding (B)</p> Signup and view all the answers

What can be concluded about enzyme specificity?

<p>Enzymes are specific for certain substrates (A)</p> Signup and view all the answers

What occurs to an enzyme when the temperature exceeds a few degrees above normal body temperature?

<p>The enzyme becomes denatured. (C)</p> Signup and view all the answers

How does decreasing the temperature affect molecular motion in reactions?

<p>Decreases molecular movement, slowing down reactions. (A)</p> Signup and view all the answers

What does 'saturation' mean in relation to enzyme activity?

<p>All enzymes in solution are occupied with substrate. (A)</p> Signup and view all the answers

What is the primary role of coenzymes in enzyme activity?

<p>They act as hydrogen carriers between enzymes. (B)</p> Signup and view all the answers

What is the significance of a zymogen in enzymatic activity?

<p>It is an inactive enzyme form activated when needed. (A)</p> Signup and view all the answers

What happens to enzymes when extreme pH changes occur?

<p>Enzymes undergo conformational changes. (C)</p> Signup and view all the answers

Why are co-factors important for enzyme activity?

<p>They assist in forming the active site. (A)</p> Signup and view all the answers

What is true about the pH optimum of enzymes?

<p>It reflects the pH of surrounding fluids. (A)</p> Signup and view all the answers

Flashcards

Transition State

The unstable state a molecule reaches when its bonds are being broken or made, allowing a reaction to occur quickly. This unstable state is caused by the enzyme.

Catalyst

A substance that speeds up a chemical reaction by lowering its activation energy but is not consumed in the reaction itself.

Activation Energy

The minimum amount of energy required for a reaction to occur.

Enzyme

A biological catalyst made of proteins that promotes a chemical reaction in living organisms.

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Active Site

The region of an enzyme that binds to the substrate and where the catalytic activity takes place.

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Substrate

The molecule an enzyme acts upon.

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Enzyme Activity

The rate at which an enzyme converts substrate to product.

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Factors Affecting Enzyme Activity

Factors that can affect how well an enzyme functions, such as temperature, pH, and concentration of cofactors and coenzymes.

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Enzyme-Substrate Complex

A temporary complex formed when the substrate binds to the active site of the enzyme.

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Enzyme Catalysis

The process by which an enzyme facilitates a chemical reaction. It involves binding the substrate to the active site, breaking and forming bonds, and releasing the product.

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Denaturation

A condition that can alter the shape and function of an enzyme, leading to a decrease in its activity. Examples include high temperatures and extreme pH values.

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Enzyme's Impact on Activation Energy

The process by which an enzyme lowers the activation energy of a reaction, making it happen much faster. It does this by providing an alternative reaction pathway with a lower energy barrier.

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What are enzymes?

Enzymes are biological catalysts that speed up chemical reactions within living organisms.

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Can enzymes be reused?

Enzymes are not consumed or changed by the reactions they catalyze, meaning they can be used repeatedly.

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Do enzymes change what happens in a reaction?

Enzymes do not change the nature of chemical reactions. They simply accelerate the rate at which they occur.

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How do enzymes make reactions faster?

Enzymes lower the activation energy of a reaction, making it easier for the reaction to start.

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What determines the shape of a protein?

The 3D shape of a protein is determined by the specific sequence of amino acids it contains.

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What is the active site of an enzyme?

The active site of an enzyme is a specific region where the substrate binds and the reaction occurs.

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What is the Lock-and-Key model?

The lock-and-key model describes the way a substrate fits perfectly into the active site of an enzyme.

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What is the Induced-Fit model?

The induced-fit model suggests that the active site can adjust itself to fit a substrate better, rather than a rigid fit.

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Enzyme Optimum Temperature

The temperature at which an enzyme functions at its highest rate.

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Enzyme Denaturation

The irreversible change in an enzyme's structure due to extreme temperatures or pH, leading to loss of function.

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Zymogen

An inactive precursor of an enzyme that can be activated when needed.

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Coenzymes

Organic molecules derived from water-soluble vitamins that assist in enzyme activity.

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Cofactors

Inorganic metal ions that aid in enzyme activity.

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Enzyme Saturation

The point at which all available enzymes are actively bound to substrate, and further increases in substrate concentration do not increase the reaction rate.

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Law of Mass Action

A reversible chemical reaction proceeds in the direction of the lower concentration of reactants or products.

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Metabolic Pathway

A series of interconnected chemical reactions, each catalyzed by a specific enzyme, that begins with an initial substrate and ends with a final product.

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Branched Metabolic Pathways

Metabolic pathways can split into multiple branches, allowing for the production of various products.

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End Product Inhibition

The accumulation of the end product of a metabolic pathway inhibits the enzyme activity at an earlier step in the pathway, regulating the overall process.

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Allosteric Inhibition

A type of end product inhibition where the product binds to the enzyme at a site other than the active site, altering the enzyme's shape and reducing its activity.

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Inborn Errors of Metabolism

Genetic defects in the genes responsible for the production of enzymes in metabolic pathways, often leading to accumulation of intermediary products or deficiency in the final product.

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First Law of Thermodynamics

Energy cannot be created or destroyed, only transformed from one form to another.

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Bioenergetics

The study of energy flow in living systems.

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Coupled Reactions: Energy Transfer

Energy that is released from breaking down molecules (like food) is used to make a readily available energy source called ATP. This means energy from exergonic reactions is transferred to the products of endergonic reactions.

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What is ATP?

The molecule that functions as a universal energy carrier within cells. It readily stores and releases energy for various cell processes.

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How is ATP made?

The process of adding a phosphate group to ADP, creating ATP. This process requires energy from exergonic reactions.

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How is energy released from ATP?

The process of breaking down ATP, releasing energy and a phosphate group, resulting in ADP. This energy is then used to power endergonic reactions.

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What is Reduction?

A chemical reaction where an atom or molecule gains electrons. This gain of electrons reduces the overall charge of the atom or molecule. (Think of it as gaining "negative" charge.)

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What is Oxidation?

A chemical reaction where an atom or molecule loses electrons. This loss of electrons increases the overall charge of the atom or molecule. (Think of it losing "negative" charge.)

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Coupled Reactions: Oxidation and Reduction

Oxidation and reduction reactions always occur together. An atom/molecule can be an oxidizing agent in one reaction and a reducing agent in another. These coupled reactions create a flow of electrons.

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Why is oxygen important in oxidation?

A very powerful oxidizing agent. This means oxygen readily accepts electrons, causing other molecules to lose electrons (be oxidized).

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Study Notes

Enzymes

  • Enzymes are biological catalysts
  • Increase the rate of a reaction
  • Not changed by the reaction (reusable)
  • Do not change the nature of the reaction
  • Lower the activation energy of the reaction

Protein Structure Revisited

  • First level: Amino acids bond to form a chain.
  • Second level: Attraction between amino acids causes pleated ribbon or coiled rod shapes.
  • Third level: Pleated ribbons and coiled rods fold into a 3D structure.
  • Fourth level: Multiple folded proteins connect to form a single protein molecule

Mechanisms of Enzyme Activity

  • Enzyme function is dictated by structure
  • Enzymes have a characteristic 3D shape with active sites
  • Reactants are called substrates
  • Original model: substrates fit into the active site (lock-and-key model)
  • Updated model: Substrate fit isn't exact, it changes shape slightly as it enters the active site (induced-fit model)
  • Enzymes are very specific to their substrates

3D Image of Enzyme Active Site

  • Protein structure supports and positions active sites.
  • Binding sites bind and orient substrates.
  • Catalytic sites reduce activation energy

Metabolic Pathways

  • Linked chemical Reactions in chains or webs.
  • Begin with an initial substrate and end with a product.
  • Involve many enzymatic steps along the way

Branched Metabolic Pathways

  • Not always linear
  • Often include branches where multiple products form

Metabolic Pathway Inhibition

  • End product inhibition occurs when the end product of a metabolic pathway blocks an earlier step in that pathway.
  • This is a form of negative feedback.
  • The end products bind to enzymes at a spot away from the active site, which alters the enzyme's shape, preventing binding to the substrate.

Inborn Errors of Metabolism

  • Gene mutations in DNA lead to flawed enzymes.
  • This impacts the pathways that follow the defective enzyme.
  • Leads to product build-up or lack of products as reactions cannot effectively proceed.
  • Can lead to fatal conditions in the fetus.

Effects of pH

  • Enzymes work best within a narrow pH range (optimum pH).
  • Extreme pH changes denature enzymes, altering their shape and function.
  • Optimum pH typically matches the pH where the enzyme functions (e.g. stomach vs saliva)

Effect of Substrate Concentration

  • Increasing substrate concentration initially increases the rate of the reaction.
  • The rate of the reaction plateaus when all enzyme active sites are continuously occupied thus reaching saturation.

Coenzymes and Cofactors

  • Coenzymes are organic molecules and cofactors are inorganic metal ions that assist enzymes in various reactions often by affecting active site shape, or assisting in temporary bonding between the enzyme and substrates.
  • Coenzymes often transport small molecules or atoms (like hydrogen)
  • Cofactors help shape the active sites of enzymes, aid in enzyme substrate bonding

Zymogens

  • Some enzymes are produced in an inactive form called zymogens.
  • The suffix -ogen helps identify these enzymes (e.g. pepsinogen).
  • Zymogens require activation via other enzymes (e.g. phosphorylation) to become active

Law of Mass Action

  • Some chemical reactions are reversible.
  • The rate of reaction depends on substrate and product concentrations.
  • Reactions tend towards the side of the reaction with the lower concentration of products/reactants.

Laws of Thermodynamics

  • First Law: Energy cannot be created or destroyed, only transferred.
  • Second Law: Energy is lost as heat, resulting in a decrease in usable energy during transformations.
  • Energy transfers are inefficient

Endergonic and Exergonic Reactions

  • Endergonic reactions require energy input to proceed.
  • Reactants have less free energy than products.
  • Exergonic reactions release energy to proceed.
  • Reactants have more free energy than products.

Coupled Reactions: ATP

  • Cells use energy stored in chemical bonds via ATP, an energy carrier
  • ATP is synthesized from ADP and phosphate using energy from exergonic reactions.
  • ATP releases energy when broken down into ADP.

Coupled Reactions: Oxidation and Reduction

  • Reactions are linked; electrons are transferred or hydrogen atoms.
  • Reduction is gaining electrons/hydrogen.
  • Oxidation is losing electrons/hydrogen.
  • Some molecules are oxidizing/reducing agents, depending on the reaction

Hydrogen Carriers

  • Coenzymes that accept/donate hydrogen atoms in redox reactions (e.g., NAD, FAD).
  • These coenzymes (NAD and FAD) play a role in energy production by carrying electrons in coupled reactions.

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