Biology Chapter: Proteins and Enzymes
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Questions and Answers

If '1' refers to nucleic acids and '2' refers to proteins, what are their corresponding structures?

  • RNA (1) and protein (2) (correct)
  • DNA (1) and RNA (2)
  • RNA (1) and DNA (2)
  • Protein (1) and RNA (2)

Which class of proteins is responsible for accelerating chemical reactions?

  • Motility proteins
  • Transport proteins
  • Enzymes (correct)
  • Structural proteins

How many different kinds of amino acids are used by the body in protein synthesis?

  • 26
  • 100
  • 20 (correct)
  • 51

What type of bond links amino acids together during polypeptide formation?

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

What is the name of process, that results in the formation of a peptide bond, with the removal of water?

<p>Dehydration (or condensation) reaction (C)</p> Signup and view all the answers

In what direction are amino acid sequences read?

<p>From the N-terminus to the C-terminus (C)</p> Signup and view all the answers

Which of the following is NOT a non-covalent bond interaction?

<p>Peptide Bond (A)</p> Signup and view all the answers

Which of the following is a multimeric protein?

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

Which of the following describes the structure of a protein consisting of two polypeptides?

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

Which of the following is the largest protein by the number of amino acids?

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

What is the primary role of an enzyme in a chemical reaction?

<p>To lower the activation energy required for the reaction (D)</p> Signup and view all the answers

Which of the following best describes the nature of the interaction between an enzyme and its substrate?

<p>Transient and reversible complexes (A)</p> Signup and view all the answers

What term is used to describe RNA molecules that have catalytic activity?

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

Which of the following statements about enzyme active sites is not true?

<p>It has the same affinity for any similar substrate. (D)</p> Signup and view all the answers

What are the nonprotein components required by some enzymes for their activity called?

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

What does the induced-fit model of enzyme-substrate interaction describe?

<p>The enzyme changes shape to optimally accommodate the substrate. (B)</p> Signup and view all the answers

How do specific noncovalent interactions contribute to enzyme catalysis?

<p>They position the substrate optimally for catalysis in the active site. (A)</p> Signup and view all the answers

Which of these is the major distinction between coenzymes and prosthetic groups?

<p>Prosthetic groups are tightly and permanently bound to the enzyme, while coenzymes are not. (B)</p> Signup and view all the answers

Which of the following is NOT a mechanism by which an enzyme increases reaction rate?

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

What is the primary distinction between a polypeptide and a protein?

<p>A polypeptide is a component of a protein, and proteins are often made of multiple polypeptides. (D)</p> Signup and view all the answers

What is a key characteristic of irreversible enzyme inhibitors?

<p>They bind to the enzyme through covalent bonds resulting in permanent inactivation. (C)</p> Signup and view all the answers

Why is proline known as a 'helix breaker' in protein structures?

<p>The rigid cyclic structure of proline's side chain prevents appropriate hydrogen bonding, essential for helix formation. (A)</p> Signup and view all the answers

If the concentration of a reversible inhibitor increases, what effect would it have on enzyme activity?

<p>The enzyme activity will decrease. (D)</p> Signup and view all the answers

Which statement best characterizes the types of bonds involved in maintaining protein structures?

<p>Covalent bonds form the primary structure, while non-covalent bonds play a crucial role in maintaining higher structural levels. (A)</p> Signup and view all the answers

How does the concentration of substrate affect available active enzyme in the context of competitive inhibition?

<p>It has a direct positive correlation with the amount of available active enzyme. (D)</p> Signup and view all the answers

What is the term for the energy stored within a system?

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

What does ∆E represent in a chemical process?

<p>The change in the internal energy of the system during the process. (D)</p> Signup and view all the answers

Which statement best describes the effect of substrate-level regulation on enzyme activity?

<p>Increased substrate leads to increased reaction rates, and increased product leads to decreased rates. (D)</p> Signup and view all the answers

A thermodynamically feasible reaction with a large negative ΔG, such as ATP hydrolysis, may not proceed at an appreciable rate because:

<p>It requires an additional input of energy for it to overcome the activation energy barrier. (B)</p> Signup and view all the answers

How is allosteric regulation different from substrate-level regulation?

<p>Allosteric enzymes are regulated by molecules binding at sites distinct from the active site. (D)</p> Signup and view all the answers

What is the purpose of feedback inhibition in an enzymatic pathway?

<p>To regulate the pathway by using the end product to inhibit the activity of an earlier enzymatic step. (D)</p> Signup and view all the answers

How is the activation energy (Eₐ) related to the rate of a reaction?

<p>The higher the activation energy, the lower the reaction rate. (C)</p> Signup and view all the answers

Why do cells not use heat to increase the kinetic energy of molecules in order to facilitate reactions?

<p>Cells need a constant temperature for their function (isothermal). (A)</p> Signup and view all the answers

Which of these is an example of irreversible covalent activation of an enzyme?

<p>Proteolytic cleavage of a zymogen. (D)</p> Signup and view all the answers

How do enzymes function as biological catalysts?

<p>By lowering activation energy required for a reaction to proceed. (C)</p> Signup and view all the answers

What happens to the catalyst itself during a chemical reaction?

<p>It remains unaltered and ready to catalyze another reaction. (A)</p> Signup and view all the answers

What is the fundamental structural unit of a macromolecule?

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

Which non-polar amino acid does not exhibit L and D isomers?

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

What is the significance of a protein's primary structure?

<p>It is directly related to the sequence of nucleotides in mRNA. (B)</p> Signup and view all the answers

How do hydrogen bonds contribute to a protein's secondary structure?

<p>They form between NH and CO groups in the polypeptide backbone. (B)</p> Signup and view all the answers

What is the specific location of R groups in an α helix?

<p>They project out from the spiral. (D)</p> Signup and view all the answers

In a β sheet, how are the R groups positioned?

<p>They project out on alternating sides of the sheet. (C)</p> Signup and view all the answers

What is the main difference between parallel and antiparallel β sheets?

<p>The direction of the polypeptide strands relative to the N- and C- termini. (C)</p> Signup and view all the answers

How does proline affect the α helix structure?

<p>It cannot form hydrogen bonds and tend to disrupt the α helix by introducing a kink or bend. (C)</p> Signup and view all the answers

What are protein motifs?

<p>Super-secondary structures composed of a few secondary structure elements. (C)</p> Signup and view all the answers

Which one best describes the tertiary structure of a protein?

<p>It is determined by the interactions of the R groups. (A)</p> Signup and view all the answers

How do fibrous proteins differ from globular proteins?

<p>Fibrous proteins possess a highly ordered and repetitive structure. (A)</p> Signup and view all the answers

Which type of protein is likely to have one or more modular units, with each module responsible for a unique function?

<p>Proteins with multiple functions each performed by a separate domain. (B)</p> Signup and view all the answers

What is the primary challenge in predicting protein tertiary structures?

<p>The complex interactions of amino acid R groups. (B)</p> Signup and view all the answers

What structural level of a protein is associated specifically with multimeric proteins?

<p>Quaternary structure. (C)</p> Signup and view all the answers

What determines the final folded shape of a protein?

<p>The protein’s primary structure (amino acid sequence). (A)</p> Signup and view all the answers

Flashcards

Protein

A biological molecule composed of amino acids linked together in a specific sequence, forming a polypeptide chain.

Amino Acids

Organic molecules that serve as the building blocks for proteins. There are 20 different amino acids, each with distinct chemical properties.

Peptide Bond Formation

The process by which amino acids are linked together to form a polypeptide chain. Involves the removal of a water molecule between each amino acid.

Primary Structure

The sequence of amino acids in a polypeptide chain. Determines the final structure and function of a protein.

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Secondary Structure

The local three-dimensional structure of a polypeptide chain, including alpha-helices and beta-sheets. Stabilized primarily by hydrogen bonds.

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Tertiary Structure

The overall three-dimensional shape of a polypeptide chain. Determined by interactions between amino acid R groups and the surrounding environment.

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Quaternary Structure

The arrangement of multiple polypeptide chains (subunits) in a multimeric protein. Involves interactions between different subunits.

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Enzymes

Proteins that act as biological catalysts, speeding up biochemical reactions without being consumed in the process.

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Structural Proteins

Proteins that provide structural support and shape to cells and tissues.

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Motility Proteins

Proteins involved in the movement of cells and organelles within cells.

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What are enzymes?

Enzymes are biological catalysts that speed up reactions by lowering the activation energy barrier.

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How do enzymes interact with substrates?

Enzymes form temporary, reversible complexes with their specific substrate molecules.

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What do enzymes do to equilibrium?

Enzymes increase the rate of a reaction but do not change the equilibrium position.

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What is the active site of an enzyme?

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

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What are cofactors?

Cofactors are non-protein molecules (like metal ions or vitamins) that are essential for the function of some enzymes.

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Why are enzymes specific?

Enzymes exhibit a high degree of specificity, meaning they typically catalyze only one or a very limited number of reactions.

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Explain the induced-fit model.

The induced-fit model describes how an enzyme's active site changes shape slightly when a substrate binds, optimizing the fit for catalysis.

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What is allosteric activation?

Allosteric activation involves a molecule binding to a site on the enzyme that is not the active site, but changes the shape of the active site to enhance its activity.

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Monomer

The fundamental building block of a macromolecule.

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Alpha Helix

A spiral structure formed by hydrogen bonding within a polypeptide chain.

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Beta Sheet

An extended, sheet-like structure formed by hydrogen bonding between polypeptide chains.

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Secondary Motif

A combination of secondary structure elements that form a specific structural motif.

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Fibrous Protein

A type of protein with a highly ordered, repetitive structure.

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Globular Protein

A type of protein with a compact, globular shape.

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Protein Domain

A functional unit within a protein, often associated with a specific activity.

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Amino Acid Sequence

The unique amino acid sequence of a protein, which is determined by the genetic code.

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Glycine

A non-polar amino acid that lacks separate L and D isomers.

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Protein Folding

The process by which a protein folds into its correct three-dimensional structure.

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Prion Protein

A type of protein that can cause misfolding and aggregation of other proteins, leading to disease.

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What is the difference between a polypeptide and a protein?

A polypeptide is a chain of amino acids linked together by peptide bonds. A protein is a polypeptide that has folded into a specific three-dimensional structure and is functional.

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Why is proline called a 'helix breaker'?

Proline's structure disrupts the formation of alpha-helices in proteins because it lacks a hydrogen atom needed for hydrogen bonding, preventing it from participating in the regular pattern required for helix formation.

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True or False: Protein structures rely solely on non-covalent bonds for secondary, tertiary, and quaternary structures.

False. While covalent bonds form the primary structure (amino acid sequence), secondary, tertiary, and quaternary structures are also influenced by covalent bonds (disulfide bridges) and non-covalent interactions like hydrogen bonds and hydrophobic interactions, contributing to their stability and shape.

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Define activation energy.

Activation energy is the minimum amount of energy that reactants (molecules involved in a reaction) must have to overcome to initiate a chemical reaction.

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What is a metastable state?

Molecules are said to be in a metastable state when they are thermodynamically unstable but kinetically stable. While a reaction might be favorable based on energy changes, it may not proceed rapidly without an energy input to overcome the activation energy barrier.

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What is meant by 'internal energy' and '∆E'?

The total energy content of a system is called internal energy (E). Changes in internal energy during a process are represented by ∆E, which is the difference in internal energy before and after the process.

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What is bond energy?

The bond energy is the amount of energy required to break a specific chemical bond. It is measured in units of calories.

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How do enzymes lower activation energy?

Enzymes can lower the activation energy by providing a suitable surface for the reactants to bind to, thus increasing the probability of collisions and facilitating the reaction.

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Induced fit

The process by which an enzyme's active site changes shape slightly to better fit the substrate, enhancing the enzyme-substrate interaction.

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Feedback Inhibition

A type of enzyme regulation where the final product of a metabolic pathway inhibits an earlier step in the pathway, preventing overproduction.

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Competitive Inhibitors

Inhibitors that bind to an enzyme's active site, competing with the substrate for binding.

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Noncompetitive Inhibitors

Inhibitors that bind to a site on the enzyme that is different from the active site, causing a conformational change that reduces the enzyme's activity.

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Transient covalent bond

The temporary covalent bond formed between an enzyme and its substrate during the reaction.

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Conformational flexibility

The enzyme's ability to change conformation, allowing it to interact with different molecules.

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Proteolytic enzyme

A protein that, once activated, can specifically cleave another protein, often activating or deactivating it.

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Zymogen

The inactive precursor form of an enzyme that is activated by proteolytic cleavage.

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Study Notes

Macromolecules - Proteins

  • Proteins are large, complex molecules crucial for various cellular functions.
  • Twenty different amino acids are used in protein synthesis.
  • Each amino acid has a similar basic structure, but the R group (side chain) varies creating differences.
  • All amino acids in human bodies are L-amino acids.
  • Proteins perform diverse functions within cells, including:
    • Enzymes: Catalysts that speed up chemical reactions.
    • Structural proteins: Provide support and shape to cells and tissues.
    • Motility proteins: Enable cellular movements.
    • Regulatory proteins: Control and coordinate cell functions.
    • Transport proteins: Move substances within and out of cells.
    • Signaling proteins: Communicate between cells.
    • Receptor proteins: Allow cells to respond to external stimuli.
    • Defensive proteins: Protect against diseases.
    • Storage proteins: Reservoirs for amino acids.
  • Protein sizes vary considerably, from the smallest at 51 amino acids (like Insulin) to the largest at 34,350 amino acids (like Titin).
  • The average protein size is about 300 amino acids.
  • There are an enormous number of possible proteins that can be combined from 20 different amino acids
  • Monomers of proteins are amino acids that are stringed together to form a polymer called a polypeptide.
  • The process of creating a polypeptide involves a dehydration reaction.
  • Polypeptides have an inherent directionality. Polypeptides are written from the N-terminus to the C-terminus.
  • The different structures of the polypeptide result from the folding of the protein, resulting in a functional protein.
    • Primary structure: The linear sequence of amino acids.
    • Secondary structure: Localized regions that form a helix or sheet through hydrogen bonds.
    • Tertiary structure: The overall three-dimensional shape of the polypeptide chain.
      • Hydrophobic interactions, the ionic bonds, hydrogen bonds, and disulfide bonds are important features in the tertiary structure
    • Quaternary structure: The arrangement of multiple polypeptide chains in a multimeric protein.
  • All amino acids, except glycine, exist as L- and D- isomers (mirrored images) - Glycine does not have separate isomers
  • Proteins with similar functions often share common domains, which are modular units that provide them with certain functions.
  • The final folded shape of a protein is determined by its primary structure.
  • There are methods for predicting the tertiary (3D) structure of a protein. One example is the AlphaFold and AlphaFold2 algorithm.
  • Some proteins are monomeric, composed of a single polypeptide chain, while others are multimeric, consisting of two or more polypeptide chains. A notable multimeric protein is Hemoglobin, consisting of 4 subunits.
  • Proteins have many different levels/organizations, with each higher-order structure relying on the lower level(s) structure
  • Enzymes are biological catalysts that lower the energy barrier for reactions to occur.
  • Enzymes have a specific active site that binds to substrates.
  • Enzymes can be regulated by factors such as temperature and pH.
  • Specific mechanisms of substrate activation include bond distortion, proton transfer, and electron transfer.
  • Proteins are subject to inhibition by molecules such as heavy metal ions, nerve gas poisons, and other chemical drugs, inhibiting their ability to function
  • Common types of inhibition include reversible and irreversible inhibition with competitive inhibitors and noncompetitive inhibitors.
  • Ways for enzymes to be regulated include:
    • Substrate-level regulation: Enzyme rates adapt to meet the needs of a cell
    • Allosteric regulation: This mode of regulation relies on interactions from molecules not substrates or products. Some enzymes have 2 different shapes that allow or disallow substrate binding and regulation.
    • Feedback inhibition: The product of a reaction inhibits an earlier step in the process to regulate the production
    • Covalent modification: Chemical groups (e.g., phosphates) are added or removed from the enzyme to modulate its activity.
    • Proteolytic cleavage: Removal of a portion of a polypeptide chain, enabling activation of otherwise inactive enzymes called zymogens

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