Protein Structure: Tertiary Bonds

Questions and Answers

What type of bond is primarily responsible for the stability of α-helices in proteins?

Hydrogen bonds (correct)

London dispersion forces

Ionic bonds

Disulfide bonds

Which of the following interactions contributes significantly to the stability of proteins, especially in their interior?

London dispersion forces (correct)

Ionic bonds

Hydrogen bonds

Covalent bonds

Why are salt bridges important in protein structure?

They are only relevant in the primary structure of proteins.

They provide strong interactions between oppositely charged groups. (correct)

They are covalent bonds that connect amino acids.

They are responsible for the secretion of proteins.

Which type of secondary structure can be formed by interactions between N−H and C=O groups of the peptide bond?

Beta sheets Signup and view all the answers

Which statement about peptide bonds is correct?

Peptide bonds are formed via dehydration condensation. Signup and view all the answers

What is the directionality of a polypeptide chain?

From amino terminal to carboxyl terminal Signup and view all the answers

Which of the following statements is true regarding secondary structure stabilization?

Hydrogen bonds can stabilize both α-helices and β-sheets. Signup and view all the answers

What primarily determines the secondary structure of a protein?

The sequence of amino acids in the primary structure Signup and view all the answers

What structural feature contributes to the distinctive properties of polypeptides?

Variable amino acid side chains Signup and view all the answers

Which type of secondary structure is characterized by a regular pattern of hydrogen bonding?

Both B and C Signup and view all the answers

What role do hydrophobic interactions play in protein structure?

They help in the folding of the protein by driving non-polar side chains together. Signup and view all the answers

What characterizes the β-sheet secondary structure?

It is stabilized by hydrogen bonds between distant amino acids. Signup and view all the answers

What is a key feature of peptide bonds in proteins?

They are less reactive compared to ester bonds. Signup and view all the answers

Which statement about the tertiary structure of proteins is correct?

It is a three-dimensional shape formed by interactions between the side chains of amino acids. Signup and view all the answers

What type of bond is primarily responsible for stabilizing the α-helix structure in proteins?

Hydrogen bonds Signup and view all the answers

What structural characteristic is common to both α-helices and β-sheets?

They are stabilized by hydrogen bonding. Signup and view all the answers

Which type of bond is formed by the oxidation of thiol groups on cysteine?

Disulfide bond Signup and view all the answers

What contributes to the apparent rarity of ionic bonds in the interior of proteins?

Most charged amino acids lie on the protein surface Signup and view all the answers

Which stabilizing bond contributes most to the overall strength of protein structure?

Disulfide bond Signup and view all the answers

What is the primary driving force behind the formation of a hydrophobic core in proteins?

Separation of non-polar molecules from water Signup and view all the answers

Which of the following interactions is NOT typically involved in stabilizing tertiary structure?

Alpha helices Signup and view all the answers

Which type of non-covalent bond involves charged amino acids positioned close together?

Ionic bonds Signup and view all the answers

How does hydrophobic bonding affect the aqueous solubility of proteins?

Increases solubility by aggregating non-polar side chains Signup and view all the answers

Which situation correctly describes the role of salt bridges in protein structure?

They occur between oppositely charged side chains. Signup and view all the answers

Which type of bond is the most significant contributor to overall protein stability?

Covalent bonds Signup and view all the answers

What is the primary role of hydrophobic interactions in protein structure?

To allow non-polar molecules to aggregate and shield from water Signup and view all the answers

What type of interactions would most likely occur in the hydrophobic core of a protein?

Hydrophobic interactions among non-polar side chains Signup and view all the answers

Which statement correctly describes ionic bonds in protein structure?

They occur between oppositely charged amino acids. Signup and view all the answers

Which of the following is NOT a characteristic of disulfide bonds?

They are present only in intracellular proteins. Signup and view all the answers

Why is ionic bonding rare in the interior of proteins?

Most charged amino acids are located on the protein surface. Signup and view all the answers

What effect do surface groups capable of forming hydrogen bonds have on protein properties?

They increase the solubility of the protein in aqueous solutions. Signup and view all the answers

What type of bond is primarily responsible for the folding and stability of extracellular proteins?

Disulfide bonds Signup and view all the answers

What mechanism primarily leads to the formation of disulfide bonds in proteins?

Oxidation of thiol groups Signup and view all the answers

Which of the following best describes the role of hydrogen bonds in the stability of β-sheets?

They are created by the interaction of N−H and C=O groups Signup and view all the answers

What is the primary structural feature of a polypeptide chain that is key for tertiary structure?

The directionality of amino acid residues Signup and view all the answers

How do hydrophobic interactions influence protein folding?

They cause hydrophobic residues to be buried in the interior Signup and view all the answers

What type of bonds is primarily responsible for stabilizing the tertiary structure of proteins in a hydrophobic environment?

Hydrophobic interactions Signup and view all the answers

What characteristic of β-sheets contributes to their stability?

Hydrogen bonding between layers of polypeptide chains Signup and view all the answers

What type of interactions are primarily responsible for the stabilization of protein structures in their interior?

Hydrophobic interactions and ionic bonds Signup and view all the answers

Which describes the role of London dispersion forces in proteins?

They provide medium-range attraction contributing to stability Signup and view all the answers

What primarily determines the secondary structure of a protein?

Hydrogen bonding between peptide NH and CO groups Signup and view all the answers

Which statement accurately describes the properties of peptide bonds?

Peptide bonds exhibit a partial double bond character Signup and view all the answers

What is characteristic of the β-sheet secondary structure?

It involves hydrogen bonding between distant parts of the polypeptide chain Signup and view all the answers

Which factor significantly influences the overall tertiary structure of a protein?

Hydrophobic interactions among nonpolar side chains Signup and view all the answers

What role do secondary structure features like loops and coils play in proteins?

They allow for flexibility and dynamic function Signup and view all the answers

Which of the following accurately describes hydrogen bonds in secondary structures?

They occur between the N−H and C=O groups of the peptide bonds Signup and view all the answers

What distinguishing characteristic of hydrophobic interactions in protein structure?

They contribute to the formation of a hydrophobic core inside the protein Signup and view all the answers

Which statement is true regarding peptide bonds in terms of reactivity?

Peptide bonds are less reactive compared to esters Signup and view all the answers

Which amino acids are typically found on the surface of proteins due to their charged side chains?

Histidine and Lysine Signup and view all the answers

What is one of the functions of globular proteins?

Defense against pathogens Signup and view all the answers

What characterizes the actin fold in proteins?

It involves ATP binding and hydrolysis across multiple subdomains. Signup and view all the answers

How do charged side chains typically behave inside a protein's structure?

They are involved in forming specific binding sites when located internally. Signup and view all the answers

Which of the following proteins is involved in the transport of molecules?

Hemoglobin Signup and view all the answers

Which type of interaction is primarily responsible for the formation of salt bridges in proteins?

Ionic interactions Signup and view all the answers

What is the primary role of polar uncharged amino acids in globular proteins?

To form hydrogen bonds, often found on the surface Signup and view all the answers

Which globular protein is primarily involved in muscle contraction?

Actin Signup and view all the answers

What role does hydroxyproline play in the structure of collagen?

It stabilizes the triple-helical structure by maximizing interchain hydrogen bonding. Signup and view all the answers

Which characteristic distinguishes elastin from collagen?

Elastin forms fibers with rubber-like properties. Signup and view all the answers

What is a common feature of collagen-related diseases like Osteogenesis imperfecta?

Mutations that replace glycine with bulky side chains in collagen. Signup and view all the answers

Which amino acid is notably absent in elastin?

Hydroxylysine Signup and view all the answers

Which statement accurately describes desmosine cross-links in elastin?

They enhance the rubber-like properties of elastin. Signup and view all the answers

How does the structure of collagen contribute to its function in connective tissue?

It forms tough fibers that withstand mechanical stress. Signup and view all the answers

What structural feature of elastin allows it to be stretched and then return to its original shape?

The desmosine cross-links that create a flexible network. Signup and view all the answers

What role does proline play in the structure of collagen?

It facilitates the formation of the helical conformation. Signup and view all the answers

Which condition leads to a fragile bone structure due to collagen mutations?

Osteogenesis imperfecta Signup and view all the answers

Which amino acid is found in every third position of the polypeptide chain in collagen?

Glycine Signup and view all the answers

What structural characteristic distinguishes collagen from most globular proteins?

Elongated, triple-helical structure. Signup and view all the answers

What amino acids are specifically mentioned as components of collagen that result from posttranslational modification?

Hydroxyproline and hydroxylysine Signup and view all the answers

In collagen, the three polypeptide chains are primarily held together by which type of interaction?

Hydrogen bonds Signup and view all the answers

How do R-groups of amino acids in collagen contribute to its structural integrity?

They promote aggregation into long fibers. Signup and view all the answers

What is the amino acid sequence pattern commonly found in collagen?

–Gly–X–Y– Signup and view all the answers

Why is the helical conformation of each alpha chain in collagen not an alpha helix?

Proline induces kinks that disrupt the α-helix structure. Signup and view all the answers

Study Notes

Tertiary Structure Stabilizing Bonds

Protein folding involves four key bonding interactions between side chains: covalent bonds, hydrophobic interactions, electrostatic interactions, and hydrogen bonding.
Disulfide bonds are formed through the oxidation of thiol (-SH) groups on cysteine, crucial for protein stability, particularly in extracellular proteins.
Ionic bonds form between oppositely charged amino acids, often located on the protein surface; interior ionic bonding is rare.
Hydrogen bonding arises from interactions between N−H and C=O groups of peptide bonds, contributing to regular structures like α-helices and β-sheets.
Hydrophobic interactions cause non-polar molecules to aggregate in aqueous solutions, forming a protective hydrophobic core within the protein.
Long-range electrostatic interactions, such as salt bridges, provide significant stability, especially when buried in hydrophobic environments.
London dispersion forces contribute medium-range weak attractions that enhance the stability of the protein's interior.

Primary Structure: The Peptide Bond

A peptide bond (amide bond) forms by linking the α-carboxyl group of one amino acid to the α-amino group of another, releasing water and resulting from a condensation reaction.
Polypeptides are chains of amino acids linked by peptide bonds, consisting of a repeating backbone and diverse side chains.
Natural polypeptides typically comprise 50 to 2000 amino acid residues, with a defined directionality from the amino terminal to the carboxyl terminal.
The backbone of polypeptides has hydrogen-bonding potential due to carbonyl groups and bonded hydrogen atoms from the amine group.
Peptide bonds exhibit stability, with lifetimes of about 1000 years in the absence of catalysts, and are kinetically stable.
The mass of proteins is measured in daltons, with 1 kDa equal to 1000 Da.

Properties of Peptide Bonds

Peptide bonds possess partial double bond character, making them rigid and nearly planar, resulting in favored trans configuration due to a large dipole moment.
The structure and properties of the protein are primarily dictated by the amino acid sequence, influencing the interactions within the polypeptide chain.
Peptide bonds are less reactive compared to esters due to resonance, providing rigidity and inhibiting rotation.

Secondary Structure: α-helix and β-sheet

Secondary structure is defined by the local spatial arrangement of the polypeptide backbone, shaped by hydrogen bonds between NH and CO groups of nearby amino acids.
Prominent secondary structures include α-helices, β-sheets, and turns, while non-repetitive structures like loops and coils also form in some regions.
The arrangement around the peptide bond and the identity of side chains are critical in determining the specific secondary structure of a protein.

Tertiary Structure Stabilizing Bonds

Protein folding involves four key bonding interactions between side chains: covalent bonds, hydrophobic interactions, electrostatic interactions, and hydrogen bonding.
Disulfide bonds are formed through the oxidation of thiol (-SH) groups on cysteine, crucial for protein stability, particularly in extracellular proteins.
Ionic bonds form between oppositely charged amino acids, often located on the protein surface; interior ionic bonding is rare.
Hydrogen bonding arises from interactions between N−H and C=O groups of peptide bonds, contributing to regular structures like α-helices and β-sheets.
Hydrophobic interactions cause non-polar molecules to aggregate in aqueous solutions, forming a protective hydrophobic core within the protein.
Long-range electrostatic interactions, such as salt bridges, provide significant stability, especially when buried in hydrophobic environments.
London dispersion forces contribute medium-range weak attractions that enhance the stability of the protein's interior.

Primary Structure: The Peptide Bond

A peptide bond (amide bond) forms by linking the α-carboxyl group of one amino acid to the α-amino group of another, releasing water and resulting from a condensation reaction.
Polypeptides are chains of amino acids linked by peptide bonds, consisting of a repeating backbone and diverse side chains.
Natural polypeptides typically comprise 50 to 2000 amino acid residues, with a defined directionality from the amino terminal to the carboxyl terminal.
The backbone of polypeptides has hydrogen-bonding potential due to carbonyl groups and bonded hydrogen atoms from the amine group.
Peptide bonds exhibit stability, with lifetimes of about 1000 years in the absence of catalysts, and are kinetically stable.
The mass of proteins is measured in daltons, with 1 kDa equal to 1000 Da.

Properties of Peptide Bonds

Peptide bonds possess partial double bond character, making them rigid and nearly planar, resulting in favored trans configuration due to a large dipole moment.
The structure and properties of the protein are primarily dictated by the amino acid sequence, influencing the interactions within the polypeptide chain.
Peptide bonds are less reactive compared to esters due to resonance, providing rigidity and inhibiting rotation.

Secondary Structure: α-helix and β-sheet

Secondary structure is defined by the local spatial arrangement of the polypeptide backbone, shaped by hydrogen bonds between NH and CO groups of nearby amino acids.
Prominent secondary structures include α-helices, β-sheets, and turns, while non-repetitive structures like loops and coils also form in some regions.
The arrangement around the peptide bond and the identity of side chains are critical in determining the specific secondary structure of a protein.

Charged Amino Acids

Arginine, histidine, lysine, aspartate, and glutamic acid are often surface-located, forming ion pairs and interacting with water.
Charged side chains may bind inorganic ions like K+, PO4^3-, and Cl- to decrease repulsion.
Charged amino acids in the protein interior typically create specific binding sites.

Polar Uncharged Amino Acids

Serine, threonine, asparagine, glutamine, tyrosine, and tryptophan are usually found on the protein surface but can also form hydrogen bonds in the interior.

Functions of Globular Proteins

Storage of Ions and Molecules: Myoglobin and ferritin.
Transport of Ions and Molecules: Hemoglobin and serotonin transporter.
Defense Against Pathogens: Antibodies and cytokines.
Muscle Contraction: Actin and myosin.
Biological Catalysis: Chymotrypsin and lysozyme.

Folds in Globular Proteins

Folds refer to larger 3D structural patterns recognized as binding sites in proteins.
Actin Fold: Involves ATP binding and hydrolysis first identified in G-actin, with four subdomains contributing to its structure.
ATP binding induces a conformational change, leading to the cleavage of ATP to ADP.

Collagen Structure

Collagen is characterized by a long, rigid triple helix formed by three polypeptides (α-chains).
Collagen includes over twenty types and features the repeating polytripeptide sequence (–Gly–X–Y–), where X is usually proline and Y is hydroxyproline or hydroxylysine.
Increased hydrogen bonding between chains contributes to structural strength.

Composition of Collagen

Proline helps create kinks in the peptide chain, preventing it from forming typical α-helices.
Glycine, the smallest amino acid, occupies every third position, facilitating the helix's compact structure.
Collagen's surface exposure allows bonding between R-groups of adjacent collagen monomers, forming long fibers.

Hydroxyproline and Hydroxylysine

Hydroxyproline and hydroxylysine, resulting from posttranslational modifications of proline and lysine, enhance collagen stability.
Hydroxyproline maximizes interchain hydrogen bonds in the collagen structure.

Elastin Structure

Elastin is a soluble protein polymer, with tropoelastin secreted into the extracellular space to interact with microfibrils like fibrilin.
Rich in proline and lysine, elastin contains little hydroxyproline and no hydroxylysine.
Elastin's unique properties include DESMOSINE cross-links, providing rubber-like elasticity.

Osteogenesis Imperfecta (OI): Also known as brittle bone syndrome, characterized by fragile bones and potential kyphotic spinal deformity.
Type II OI is lethal; severe cases often involve mutations in type I collagen genes.
Mutations may replace glycine with bulkier residues, disrupting triple helix formation and structural integrity.

Studying That Suits You

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

Description

Explore the critical stabilizing bonds in protein tertiary structure through this quiz. Learn about the roles of covalent bonds, hydrophobic interactions, electrostatic interactions, and hydrogen bonding in maintaining protein stability. Test your understanding of how these interactions contribute to the overall 3D shape of proteins.