Peptide Bond Resonance: Amino Acid Conformations Quiz and Flashcards

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Questions and Answers

Which type of interaction is stronger than H-bonds and can extend over greater distances?

Dipole-dipole interactions

Hydrophobic interactions

Van der Waals forces

Charge-charge interactions (correct)

What is the main reason for the poor solubility of substances with hydrophobic interactions?

Formation of strong hydrogen bonds with water

Absence of polar bonds that can interact with water molecules (correct)

Increase in entropy upon dissolution

Interaction with other nonpolar groups in solution

What type of molecules contain both polar and nonpolar regions, exhibiting distinct properties?

Hydrophilic molecules

Amphipathic molecules (correct)

Amphoteric molecules

Hydrogen bond forming molecules

In the context of water dissociation, what does a low pH value indicate?

High concentration of H+ ions Signup and view all the answers

Which concept describes water as a proton donor and has a conjugate base when deprotonated?

Bronsted acid concept Signup and view all the answers

What does the Henderson-Hasselbalch equation help determine in weak acid solutions?

$\text{pH}$ at equilibrium Signup and view all the answers

Which factor contributes to the distinct cis and trans conformations of peptide groups?

Double bond character around the C-N linkage Signup and view all the answers

Why is the cis conformation of peptide groups less favorable than the trans conformation?

Because of steric interference of alpha-carbon side chains Signup and view all the answers

What restricts the rotation of the N-Calpha bond in proline?

The ring structure of proline Signup and view all the answers

What type of trajectory do alpha atoms follow in an alpha helix?

Cork screw trajectory Signup and view all the answers

What stabilizes an alpha helix through many nearly parallel interactions?

Hydrogen bonds Signup and view all the answers

What defines the pitch of an alpha helix in terms of its geometry?

Advance along the helix long axis per turn Signup and view all the answers

What is the main role of Na+-K+ ATPase in active transport?

Maintaining a Na+ gradient in animals Signup and view all the answers

How does the flow of Na back down its concentration gradient contribute to active transport?

Releases energy to drive glucose transport against its concentration gradient Signup and view all the answers

What is the function of nitrogenase in the production of ammonia?

Catalyzing the reaction between nitrogen and hydrogen Signup and view all the answers

How do enzymes facilitate reactions?

By providing an active site for substrate binding and product conversion Signup and view all the answers

In terms of structure, what can enzymes consist of?

Single proteins or multiple subunits (polypeptides) Signup and view all the answers

What effect do catalysts, such as enzymes, have on reactions?

Speed up attainment of reaction equilibrium without affecting equilibrium itself Signup and view all the answers

What does the kcat/Km value indicate about an enzyme reaction?

The catalytic efficiency of the enzyme Signup and view all the answers

In the Lineweaver-Burk plot, what does the slope represent?

Km/vmax Signup and view all the answers

What type of reactions do lyases catalyze?

Cleavage reactions leaving a double bond Signup and view all the answers

Which class of enzymes catalyzes oxidation-reduction reactions?

Oxidoreductases Signup and view all the answers

What is the largest class of enzymes based on their abundance?

Hydrolases Signup and view all the answers

Which enzyme classification includes enzymes that catalyze group transfer reactions?

Transferases Signup and view all the answers

At what pH does an amino acid exist in a zwitterion form?

7 Signup and view all the answers

What is the distinguishing feature of proline among amino acids?

Contains a heterocycle Signup and view all the answers

Which amino acid forms disulfide bonds to stabilize extracellular proteins?

Cysteine Signup and view all the answers

What is the pH range at which acidic amino acids like aspartic acid (D) and glutamic acid (E) exhibit strong H-bonding abilities?

4-5 Signup and view all the answers

Which amino acid can coordinate with metal ions and exhibit hydrogen bonding?

Histidine Signup and view all the answers

Which characteristic differentiates basic amino acids from other types of amino acids?

"Basic" side chains with nitrogen atoms having free electron pairs Signup and view all the answers

What is the primary function of proteins according to the text?

"Signalling" Signup and view all the answers

In what form does the polypeptide chain of a protein fold under physiological conditions?

"Native conformation" Signup and view all the answers

"Peptide bonds eliminate the ionizable alpha-carboxyl groups of free amino acids." This statement emphasizes what aspect of peptide bond formation?

"Condensation reaction" Signup and view all the answers

Study Notes

Non-Covalent Interactions

Hydrogen bonds (H-bonds) are strong if all three atoms are aligned
H-bonds are classified into two main types: hydrogen donors (imino and hydroxyl groups) and hydrogen acceptors (three types)
Charge-charge interactions: electrostatic interactions between opposite charges, stronger than H-bonds, and can extend over greater distances
Van der Waals forces: weak interactions between permanent or induced dipoles, only work at short optimal distances, but a large number of interactions add up to a significant stabilizing force
Hydrophobic interactions: few or no polar bonds, cannot engage in hydrogen bonds with water molecules, poorly soluble, and increase in entropy

Water and Solubility

Water is a dipole, allowing it to form hydrogen bonds with itself
The stronger the polarity, the more soluble
Polar water molecules align themselves around polar molecules, making solvation energetically favorable
Solvation is favored over the crystal lattice, and ions dissolve
The organization of the hydration shell is energetically favorable

Dissociation of Water and Acids

Water dissociation: pH = -log10(H+), pH + pOH = 14
The Brønsted acid concept: water as a proton donor and acceptor
Dissociation of strong and weak acids
pH of weak acid solutions: Henderson-Hasselbalch equation
Buffer function: ability to resist changes in pH when acid or base is added

Amino Acids

Central dogma of molecular biology: DNA → RNA → protein
Proteins are built from 20 building blocks (amino acids)
Protein functions: enzymatic reactions, transport, carrier proteins, channels, structural proteins, motor, gene expression, signaling, defense, and attachment
Amino acid structure: amino group, carboxyl group, R group, and alpha carbon atom
Amino acids carry both negative and positive charges, forming a zwitterion
Alpha carbon is chiral/asymmetric, and stereochemistry of amino acids is important
Individual properties of amino acids: aliphatic, aromatic, sulfur-containing, basic, acidic, amides, and alcohols

Primary and Secondary Structure

Primary structure: the linear sequence of amino acids, unique sequence for a protein
Peptide bonds link amino acids in proteins, forming a peptide chain
Formation of peptide bonds eliminates the ionizable alpha-carboxyl groups of free amino acids
Polypeptide chain nomenclature: each amino acid subunit of a protein is one residue
Four levels of protein structure: primary, secondary, tertiary, and quaternary

Conformational Properties of the Polypeptide Chain

Factors contributing to protein structure: allowable bond rotations, weak non-covalent interactions between backbone and sidechain groups
Peptide group: atoms lie in one plane, and the C-N peptide bond has double bond character
Trans and cis conformations of a peptide group: trans is more favorable due to steric interference
Rotation of bonds in a peptide chain: restricted by steric interference between main chain and side chain atoms
The Ramachandran plot: a 2D representation of the phi and psi angles, showing the allowed regions of the plot

Secondary Structure - Alpha Helices

Secondary structure: regularly repeating conformations of the polypeptide backbone
Alpha helix: a right-handed helix, stabilized by many hydrogen bonds, with a dipole moment
Pitch of the helix: the advance along the helix long axis per turn

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Description

Test your knowledge on the C-N peptide bond in amino acids, including its double bond character due to resonance and the resulting effects on bond rotation and atom plane alignment. Explore the differences between the trans and cis conformations of peptide groups, and learn about the factors that make the cis conformation less favorable than the trans conformation.

Amino Acid Peptide Bond Resonance and Conformations Quiz