Protein Structure and Function Quiz
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Questions and Answers

What is the total number of amino acids present in a tripeptide?

  • Three (correct)
  • Four
  • Five
  • Two

Which bond in the main chain of a peptide can freely rotate?

  • Alpha carbon to nitrogen (correct)
  • Carbonyl carbon to carbonyl oxygen
  • Peptide bond
  • Beta carbon to alpha carbon

Why can't the peptide bond freely rotate?

  • It lacks hydrogen bonding
  • It is sp2 hybridized and shows resonance (correct)
  • It is centrally positioned in the molecule
  • It is sp3 hybridized

Which of the following describes the electron state of nitrogen (N) when it has 3 bonds?

<p>It is neutral with no charge (C)</p> Signup and view all the answers

Which atom is considered the nucleophile during a hydrolysis reaction of a dipeptide?

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

Which groups must be identified when drawing a tripeptide?

<p>Peptide plane and hydrogen bond donors/acceptors (C)</p> Signup and view all the answers

In a peptide plane, which of the following six atoms are present?

<p>Carbonyl carbon, carbonyl oxygen, nitrogen, its attached hydrogen, two alpha carbons (D)</p> Signup and view all the answers

What happens to the lone pair of electrons on nitrogen when it forms three bonds?

<p>It is released, leading to a positive charge (B)</p> Signup and view all the answers

What drives the clustering of hydrophobic molecules in water?

<p>Strong bonding between water molecules (C)</p> Signup and view all the answers

What is released when hydrophobic molecules cluster together?

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

Which term refers to the phenomenon driving the aggregation of hydrophobic molecules?

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

Which type of non-covalent interaction is primarily related to the interaction of aromatic rings?

<p>Van der Waals interactions (C)</p> Signup and view all the answers

What is the role of water molecules surrounding hydrophobic molecules?

<p>To create an ordered state and restrict movement (C)</p> Signup and view all the answers

How does the removal of a negatively charged amino acid affect the folding reaction's equilibrium constant (Keq)?

<p>It increases Keq by stabilizing the folded state (D)</p> Signup and view all the answers

What charge should the central nitrogen have in the resonance structure of a peptide bond?

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

Which of the following structures is similar to a clathrate cage formed by water?

<p>Ice-like structure (B)</p> Signup and view all the answers

Which molecule is described as having a symmetrical arrangement that makes it nonpolar?

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

What is the Gibbs free energy change ($ riangle G$) for a spontaneous reaction?

<p>$-5$ kJ mole-1 (C)</p> Signup and view all the answers

Which type of non-covalent bond is characterized by interactions between charged particles?

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

In the context of macromolecular structure, which two interactions are more closely related?

<p>Hydrophobic interactions and Van der Waals forces (C)</p> Signup and view all the answers

What does a higher activation energy indicate about a chemical reaction?

<p>The reaction is less spontaneous (B)</p> Signup and view all the answers

Which of the following statements is true regarding macromolecules and non-covalent bonds?

<p>Macromolecules can utilize multiple weak bonds for flexibility (A)</p> Signup and view all the answers

Which molecule is likely to have the highest partial positive charge?

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

Which type of interaction is typically important in the core of a protein?

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

What is the correct order of atoms when describing the first amino acid in a tripeptide?

<p>Alpha carbon, carbonyl carbon, carbonyl oxygen, nitrogen, amide proton (D)</p> Signup and view all the answers

How should amino acid sequences be written?

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

How many alpha carbons are present in the tripeptide A-G-A?

<p>3 alpha carbons (C)</p> Signup and view all the answers

What is the role of the alpha carbon in an amino acid?

<p>It is the carbon directly adjacent to the carbonyl carbon (D)</p> Signup and view all the answers

In a tripeptide, how many peptide bonds exist?

<p>2 peptide bonds (A)</p> Signup and view all the answers

How should all main chain atoms in a peptide plane be represented?

<p>In a cis conformation on the paper (C)</p> Signup and view all the answers

What is the general rule for the number of peptide planes in a tripeptide?

<p>Equal to the number of peptide bonds (D)</p> Signup and view all the answers

In a peptide plane, how should atoms be visually represented?

<p>Atoms should be enclosed in a dashed box (A)</p> Signup and view all the answers

What occurs to energy when a bond is broken?

<p>Energy is required to break the bond. (A)</p> Signup and view all the answers

In the dissociation reaction H3O+ + OH- ↔ 2H2O, what does it mean for the reaction to be at equilibrium?

<p>The rates of the forward and reverse reactions are equal. (A)</p> Signup and view all the answers

If the equilibrium constant (Keq) for a reaction is less than 1, what does this indicate about the reaction?

<p>The reaction is unfavorable and favors reactants. (C)</p> Signup and view all the answers

What is true about the relationship between Delta G and protein stability?

<p>A negative Delta G indicates a more stable protein. (A)</p> Signup and view all the answers

Can the equilibrium constant (Keq) be negative?

<p>No, because concentrations are always positive. (B)</p> Signup and view all the answers

In the context of bond

<p>Energy is needed for bond breaking and allows lower energy to be formed. (D)</p> Signup and view all the answers

Which of the following equations represents the thermodynamic rule of thumb?

<p>Delta G = G* - RTln[P]/[R] (C)</p> Signup and view all the answers

What happens to bond stability during bond swapping in cells?

<p>Bonds form and break at constant rates. (A)</p> Signup and view all the answers

Which reaction is spontaneous based on the equilibrium constant (Keq) values?

<p>Reaction A, as Keq is greater than 1 (C)</p> Signup and view all the answers

What does a reaction with a Keq of less than 1 indicate?

<p>It favors reactants over products (C)</p> Signup and view all the answers

Why is ATP hydrolysis considered irreversible?

<p>Manipulation of the ratio of products to reactants is ineffective (A)</p> Signup and view all the answers

What role does Le Chatelier's principle play in reaction dynamics?

<p>It predicts shifts in equilibrium when conditions change (D)</p> Signup and view all the answers

In the context of metabolic pathways, which statement is true?

<p>Metabolic needs can change the direction of reactions (C)</p> Signup and view all the answers

What happens to a reaction that is displaced from equilibrium?

<p>It requires energy input to return to equilibrium (D)</p> Signup and view all the answers

What is the significance of labeling reactants and products in a progress curve?

<p>It distinguishes the starting materials from the final outcome (C)</p> Signup and view all the answers

What is indicated by a reaction that requires an input of energy to continue?

<p>It is an endergonic reaction (D)</p> Signup and view all the answers

Flashcards

Valence Electrons

The ability of an atom to form bonds with other atoms by sharing or gaining electrons. It is determined by the number of electrons in the outermost energy level (valence shell) of an atom.

Coordinate Covalent Bond

A bond where one atom donates a pair of electrons to another atom. It is a type of covalent bond where the shared electron pair comes completely from one of the atoms.

Cation

A positively charged ion that forms when a neutral atom loses one or more electrons. It is an atom that has lost electrons.

Anion

A negatively charged ion that forms when a neutral atom gains one or more electrons. It is an atom that has gained electrons

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Protonation

When a molecule gains a proton (H+). It occurs when a proton is added to an atom in a molecule, usually a nitrogen or oxygen.

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Zwitterion

A molecule that has both a positive and a negative charge on different parts of the molecule.

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Hydrolysis

The chemical reaction that breaks apart a peptide bond by adding water. Its the reverse of condensation.

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Condensation

The chemical reaction that forms a peptide bond between two amino acids by releasing a molecule of water.

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Alpha Carbon

The carbon atom directly attached to the carbonyl group (C=O) in an amino acid.

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Peptide Bond

The bond between the carbonyl carbon of one amino acid and the nitrogen of the next amino acid, forming the backbone of a protein.

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Peptide Plane

The arrangement of the atoms in a peptide bond (carbonyl carbon, nitrogen, alpha carbon of the next amino acid) that lies in the same plane.

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N-terminus

The end of a polypeptide chain that contains a free amino group (-NH2).

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C-terminus

The end of a polypeptide chain that contains a free carboxyl group (-COOH).

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Tripeptide

A sequence of three amino acids linked by peptide bonds.

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Amino Acid Sequence

The arrangement of amino acids in a protein chain, written from the N-terminus to the C-terminus.

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Cis Conformation

A conformation where the atoms in a peptide plane are all oriented in the same plane, similar to a flat sheet.

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Hydrogen bond

A type of non-covalent interaction in which a hydrogen atom is shared between two electronegative atoms, such as oxygen or nitrogen.

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Ionic bond

An electrostatic interaction between oppositely charged ions.

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Hydrophobic interaction

A type of non-covalent interaction that occurs between nonpolar molecules in an aqueous environment.

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Van der Waals forces

Weak, short-range interactions that arise due to temporary fluctuations in electron distribution.

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Gibbs free energy change (ΔG)

The energy change accompanying the reaction, indicating whether the reaction is spontaneous or not.

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Activation energy (Ea)

The minimum amount of energy required for reactants to reach the transition state and proceed with the reaction.

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Reaction coordinate diagram

A visual representation that shows the energy changes during a reaction, including the activation energy and the difference in energy between reactants and products.

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Spontaneous reaction

A reaction that occurs spontaneously, releasing free energy and having a negative Gibbs free energy change.

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Hydrophobic Effect

The tendency of nonpolar molecules to cluster together in an aqueous environment, driven by the increased entropy of water molecules when they are released from the hydrophobic molecule's hydration shell.

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Clathrate Cage

A three-dimensional, cage-like structure formed by water molecules surrounding a nonpolar molecule. It is a highly ordered structure, with decreased entropy compared to bulk water.

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Van der Waals Interactions

A type of non-covalent interaction between nonpolar molecules, especially aromatic rings, based on the attraction between temporary dipoles generated due to fluctuating electron clouds. It is important in stacking interactions in DNA and protein folding.

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Dipole-Charge Interaction

A type of non-covalent interaction between an ion and a polar molecule, where the partial charges of the polar molecule interact with the full charge of the ion.

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Salt Bridge

A type of non-covalent interaction between two oppositely charged ions, where the positive charge of one ion interacts with the negative charge of the other ion.

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Folded State (Protein)

The state of a molecule where its atoms are in a fixed arrangement, typically with a specific three-dimensional shape.

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Unfolded State (Protein)

The state of a molecule where its atoms are not in a fixed arrangement, and the molecule is more flexible and loosely organized.

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Bond Breaking Requires Energy

The process of breaking a chemical bond requires energy. This energy is used to overcome the attraction between the atoms in the bond. When the bond breaks, the resulting fragments can then form new, lower energy bonds, releasing energy in the process.

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What is Equilibrium?

Equilibrium in a chemical reaction means that the rate of the forward reaction (reactants to products) is equal to the rate of the reverse reaction (products to reactants). This doesn't mean the reaction stops, but that the concentrations of reactants and products remain constant.

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Keq < 1: Unfavorable Reaction

A reaction with a Keq (equilibrium constant) less than 1 favors the reactants. This means at equilibrium, there will be more reactants than products, indicating the reaction is unfavorable.

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Can Keq be Negative?

Keq, being a ratio of concentrations, cannot be negative. Concentrations are always positive values.

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Thermodynamic Rule of Thumb

The thermodynamic rule of thumb relates the change in free energy (Delta G) to the equilibrium constant (Keq) and temperature. It helps predict whether a reaction will be spontaneous (favorable) or not.

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Protein Stability

The thermodynamic rule of thumb can be applied to protein stability by looking at the free energy difference between the folded and unfolded states of a protein. A more negative Delta G indicates a stable protein.

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Free Energy Plot

A free energy (Gibbs free energy) plot shows the energy changes throughout a chemical reaction, from reactants to products. The reaction coordinate is a representation of the progress of the reaction.

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Keq > 1: Favorable Reaction

A chemical reaction with a Keq greater than 1 favors the formation of products at equilibrium. This means there will be more products than reactants, indicating a favorable reaction.

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Non-Spontaneous Reaction

A reaction where the change in Gibbs free energy is positive, meaning it requires energy input to occur.

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Equilibrium

The point where the rates of the forward and reverse reactions of a reversible reaction are equal, leading to a constant concentration of reactants and products.

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Equilibrium Constant (Keq)

The ratio of products to reactants at equilibrium, indicating the extent to which a reaction proceeds to completion.

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Near-Equilibrium Reaction

A reaction where the change in Gibbs free energy is close to zero, meaning it is easily reversible and can shift in either direction depending on the conditions.

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Activation Energy

The energy required to start a chemical reaction, even if it is spontaneous.

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Reaction Quotient (Q)

The ratio of products to reactants at any given time, not necessarily at equilibrium.

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Le Chatelier's Principle

A principle that states that a system will shift to relieve stress when a change in conditions is applied, such as adding reactants.

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Study Notes

Protein Structure and Function

  • Proteins play a dominant role in cell function, requiring knowledge of their chemical structure and single/three-letter names of the twenty standard amino acids
  • Amino acids should be drawn with appropriate charges at pH 2.0, 7.0, and 12.0 in aqueous solutions.
  • The pKa values for the main chain carboxy and amino groups are 3.0 and 9.0, respectively, and Lehninger provides the pKa of the R-groups.

Water as a Solvent

  • Water's polarity allows it to dissolve various substances (sugars, amino acids, salts) due to hydrogen bonding and ion-dipole interactions.
  • Water's ability to make hydrogen bonds and solvate ions makes it a great solvent for life.
  • Hydrophobic molecules cluster together in water to minimize their interaction with the polar water molecules.

Non-Covalent Interactions

  • Four types of non-covalent bonds facilitate macromolecular structure and function: hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces.
  • Hydrogen bonds and ionic bonds relate strongly due to their electrostatic nature involving H and O, N, and F.
  • Hydrophobic interactions are prevalent in protein cores because hydrophobic amino acids minimize their interaction with water.

Peptide Bond Resonance

  • The peptide bond exhibits resonance structures, influencing the peptide plane and limiting rotation.
  • For correct resonance structures, nitrogen should have a positive charge, while the left-side alpha-carbon should have an R-group attached.

Tripeptides

  • A tripeptide contains three amino acids linked by peptide bonds.
  • The peptide plane involves specific atoms, and there should be a dashed box enclosing the atoms within the plane.
  • The main chain bonds can rotate freely, except for the peptide bond.

Equilibrium and Reaction Rates

  • Equilibrium is reached when the rates of the forward and reverse reactions are equal, and the relative concentrations of reactants and products remain constant
  • The rate-limiting step of a reaction is the highest energy peak on a reaction coordinate graph, representing the transition state. Transition states have high energy.
  • The rate of a reaction also depends on factors like temperature due to kinetics and thermodynamics.

Thermodynamics and Protein Folding

  • Folding reactions are spontaneous, with negative ∆G.
  • The thermodynamic "rule of thumb" relating to dG involves the concentrations of products and reactants relative to equilibrium.
  • ΔG, ΔH, and ΔS are needed to assess spontaneity at different temperatures.

Quiz Questions and Answers

  • Specific questions and answers about free energy diagrams are included, emphasizing energy changes, spontaneity, and the role of equilibrium constants.

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Description

This quiz covers essential concepts related to protein structure and function, including the roles of amino acids, the properties of water as a solvent, and non-covalent interactions that influence macromolecular structures. Test your knowledge on the pH effects, pKa values, and interaction types that are critical for life processes.

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