Biochemistry Chapter on Peptide Bonds

Podcast Beta

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What is the primary structural characteristic of parallel β sheets?

They consist of strands running in opposite directions.

They have linear hydrogen bonds.

They exhibit a longer repeat period than antiparallel β sheets.

They have bent hydrogen bonds due to strands running in the same direction. (correct)

Which amino acids are commonly found in β-turns, specifically at positions 2 and 3?

Thr and Val

Ala and Ser

Gly and Pro (correct)

Lys and Asn

What is the result of the orientation of strands in antiparallel β sheets?

Their repeat period is shorter compared to parallel β sheets.

They require more amino acids for a complete turn.

Shorter hydrogen bonds lead to weaker bonding.

Linear hydrogen bonds contribute to a stronger structure. (correct)

What geometric arrangement is created by the tetrahedral geometry of the α-carbon in the peptide bond?

Pleated sheet-like structure. Signup and view all the answers

In which scenario do β-turns occur within protein structures?

When β sheets change directions. Signup and view all the answers

What primarily holds the interacting segments of polypeptide chains in their characteristic positions within the tertiary structure of a protein?

Weak interactions and disulfide covalent bonds Signup and view all the answers

What defines the quaternary structure of a protein?

The 3D arrangement of multiple polypeptide chains Signup and view all the answers

Which structural feature enhances the strength of α-keratin?

Covalent cross-links formed by disulfide bonds Signup and view all the answers

Which of the following best describes fibrous proteins?

They primarily consist of a single type of secondary structure. Signup and view all the answers

Which specific biochemical process can alter the structure of α-keratin?

Permanent waving through moisture and heat Signup and view all the answers

What process involves the loss of protein structure resulting in loss of function?

Denaturation Signup and view all the answers

Which of the following factors can induce protein denaturation?

Reduced pH Signup and view all the answers

Which structure is primarily encoded in the amino acid sequence of proteins?

Primary structure Signup and view all the answers

What is a potential consequence of protein misfolding and aggregation in the human body?

Formation of amyloid fibrils Signup and view all the answers

What type of proteins includes keratin and collagen?

Fibrous proteins Signup and view all the answers

What effect does the resonance hybrid nature of the peptide bond have?

Rigidity and slight flexibility in structure Signup and view all the answers

Which angles correspond to the rotation around the alpha carbon in a fully extended polypeptide?

180° for both phi and psi Signup and view all the answers

Which secondary structure is primarily stabilized by hydrogen bonds between nearby residues?

α-helix Signup and view all the answers

Which amino acid is known to act as a helix breaker due to its unique side chain properties?

Proline Signup and view all the answers

What is the common arrangement of residues in the α-helix structure?

Hydrogen bonds between the carbonyl oxygen of one amino acid and the amide nitrogen of another four residues away Signup and view all the answers

What does the term 'random coil' refer to in the context of peptide structure?

An irregular arrangement of the polypeptide chain Signup and view all the answers

Which dihedral angles are typically represented on a Ramachandran plot?

Phi (ϕ) and psi (ψ) angles Signup and view all the answers

What is the relationship between the side chains of amino acids and the stability of α-helices?

Attractive or repulsive interactions between side chains 3-4 residues apart influence stability Signup and view all the answers

How many residues per turn does a right-handed α-helix typically contain?

3.6 residues Signup and view all the answers

What primarily defines the secondary structure of proteins?

Local spatial arrangement of the polypeptide backbone Signup and view all the answers

What is the primary amino acid composition of collagen?

35% Gly, 21% Pro Signup and view all the answers

What is the structural arrangement of the collagen molecules?

Three polypeptides super-twisted in a unique structure Signup and view all the answers

What is the role of ascorbic acid (vitamin C) in collagen synthesis?

It acts as a coenzyme for proline hydroxylase Signup and view all the answers

How many alpha helices does myoglobin contain?

8 alpha helices Signup and view all the answers

What prevents the oxidation of Fe2+ in myoglobin?

The hydrophobic environment created by α-helices Signup and view all the answers

What is not a characteristic of the collagen structure?

Single polypeptide chain Signup and view all the answers

Which protein has the highest proportion of α-helix as shown in the provided data?

Myoglobin Signup and view all the answers

What happens to Fe2+ in the presence of water?

It oxidizes to Fe3+ and cannot bind O2 Signup and view all the answers

Study Notes

Peptide Bond Structure

The peptide bond is a covalent bond formed between the carboxyl group of one amino acid and the amino group of another.
The peptide bond is a resonance hybrid, meaning it can exist in two different forms that contribute to its overall structure.
This resonance contributes to the peptide bond's rigidity, planarity, and low reactivity.
The peptide bond is less reactive compared to esters due to resonance.
The peptide bond exhibits a large dipole moment in the favored trans configuration.

Dihedral Angles and Ramachandran Plots

Rotation around the peptide bond itself is not permitted.
Rotation around bonds connected to the alpha carbon is permitted.
Phi (Φ) is the angle around the α-carbon-amide nitrogen bond.
Psi (Ψ) is the angle around the α-carbon-carbonyl carbon bond.
In a fully extended polypeptide, both Φ and Ψ are 180°.
Some combinations of Φ and Ψ are unfavorable due to steric clashes between atoms.
Other combinations are favorable due to the potential for hydrogen bond formation.
Ramachandran plots show the possible Φ and Ψ combinations for different amino acids.

Secondary Structures

Secondary structure refers to the local spatial arrangement of the polypeptide backbone.
Common secondary structures include alpha helices and beta sheets.
Alpha helices are stabilized by hydrogen bonds between nearby residues.
Beta sheets are stabilized by hydrogen bonds between adjacent segments that may not be nearby.
Irregular arrangements of the polypeptide chain are called random coils.
Secondary structure can be determined experimentally through circular dichroism spectroscopy.

Alpha Helices

The alpha helix is a right-handed helix with 3.6 residues per turn.
Peptide bonds are aligned roughly parallel to the helical axis.
Side chains point out and are roughly perpendicular to the helical axis.
The helix is stabilized by hydrogen bonds between the backbone amides of an n and n+4 amino acid.
Alpha helix formation can be affected by the size and properties of amino acid side chains.

Beta Sheets

Beta sheets are formed by hydrogen bonds between the backbone amides of different polypeptide strands.
Beta sheets can be parallel or antiparallel.
Parallel beta sheets have a shorter repeat period (6.5 Å) and weaker hydrogen bonds.
Antiparallel beta sheets have a longer repeat period (7 Å) and stronger hydrogen bonds.
Beta turns are commonly found at the surface of proteins.
They are 180° turns that involve four amino acids.
Glycine and proline are often found in beta turns.

Tertiary Structure

Tertiary structure refers to the overall three-dimensional arrangement of all atoms in a protein.
Tertiary structure is determined by interactions between amino acids that may be far apart in the polypeptide sequence.
Interactions that contribute to tertiary structure include hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bridges.
Globular proteins are characterized by their compact, rounded shapes.

Quaternary Structure

Quaternary structure refers to the arrangement of multiple polypeptide chains (subunits) in a protein complex.
Quaternary structure is essential for the function of many proteins.
Fibrous proteins are elongated and often have structural roles.
Examples of fibrous proteins include α-keratin, collagen, and silk fibroin.

Structure of α-Keratin

α-keratin is found in hair, wool, nails, claws, and other structures that require strength.
It consists of two α-helices that assemble into a coiled coil.
Coiled coils further assemble into protofilaments and protofibrils.
Disulfide bonds stabilize the quaternary structure of α-keratin.

Structure of Collagen

Collagen is found in connective tissues, cartilage, tendons, and bone.
It contains a high proportion of glycine, proline, and hydroxyproline.
Collagen is a left-handed helix with three amino acids per turn.
Three separate polypeptide chains are super-twisted about each other.
Collagen fibrils are cross-linked by imine bonds between modified lysine and hydroxylysine residues.

Structure of Myoglobin

Myoglobin is a globular protein that binds oxygen.
It consists of a single polypeptide chain and a heme group.
The heme group contains an iron atom that binds oxygen.
The heme group is located in a hydrophobic crevice to prevent oxidation of the iron atom.

Protein Denaturation

Protein denaturation is the loss of protein structure and function.
Denaturation can be caused by heat, extreme pH, organic solvents, detergents, and other factors.
Denaturation disrupts the non-covalent interactions that hold the protein together.

Protein Renaturation

In some cases, denatured proteins can refold back to their native conformation after removal of the denaturant.
This process is called renaturation.
Renaturation demonstrates that the tertiary structure of a protein is encoded in its amino acid sequence.

Protein Folding

Protein folding is a complex and highly regulated process.
Protein folding is guided by the interactions between amino acids in the polypeptide chain.
Chaperone proteins assist in protein folding.

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Description

Explore the structure and properties of peptide bonds in biochemistry. This quiz covers the formation, rigidity, and behavior of peptide bonds, as well as the significance of dihedral angles and Ramachandran plots in protein structures. Test your understanding of how these concepts influence protein conformation.