Protein Structure: Primary and Secondary

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Questions and Answers

What does the 1° structure of a protein refer to?

The quaternary structure of a protein

The local conformations of a protein

The sequence of amino acids in a polypeptide chain (correct)

The 3D conformation of a protein

What type of bonds are involved in the formation of α-helices?

Ionic bonds

Disulfide bonds

Hydrogen bonds (correct)

Peptide bonds

Which of the following is a characteristic of α-helices?

Random coil structure

Helical structure (correct)

β-turns

Extended flat sheets

What is the direction of the hydrogen bonds in an α-helix?

Parallel to the axis of the helix Signup and view all the answers

Which two bonds have free rotation in a protein?

Bonds between α-carbon and amino nitrogen, and bonds between α-carbon and carboxyl carbon Signup and view all the answers

What is the type of structure that involves extended, flat sheets?

β-Sheet Signup and view all the answers

How many amino acids down the chain does the C=O of one amino acid hydrogen bond to in an α-helix?

Four Signup and view all the answers

What is the average number of amino acids in each turn of the α-helix?

3.6 Signup and view all the answers

What is the secondary structure element that involves a regular pattern of hydrogen bonds between amide N-H and C=O groups?

All of the above Signup and view all the answers

Why does proline create a bend in the α-helix structure?

Due to the restricted rotation of its cyclic structure and lack of N-H for hydrogen bonding Signup and view all the answers

What is the main difference between globular and fibrous proteins?

Globular proteins are soluble in water, while fibrous proteins are not Signup and view all the answers

What is the term for the local conformations maintained by extensive hydrogen bonding in a protein?

Secondary structure Signup and view all the answers

Which of the following is NOT a type of secondary structure?

Quaternary structure Signup and view all the answers

What is the term for the association of polypeptide chains?

Quaternary structure Signup and view all the answers

What is the effect of the presence of BPG on hemoglobin's affinity for oxygen?

It decreases the affinity Signup and view all the answers

What is the purpose of hemoglobin in the blood?

To transport oxygen from the lungs to the tissues Signup and view all the answers

What is the main cause of denaturation?

pH changes, mercaptoethanol, detergent, heat, and urea/guanidine Signup and view all the answers

What is the result of heat-induced denaturation of proteins?

Exposure of nonpolar segments to aqueous solvent Signup and view all the answers

What is the effect of 2,3BPG on hemoglobin?

It decreases the affinity of hemoglobin for oxygen Signup and view all the answers

What is the term for the change in the oxygen binding behavior of hemoglobin in response to changes in pH and CO2 levels?

Bohr effect Signup and view all the answers

What is the function of molecular chaperones?

To restore misfolded proteins Signup and view all the answers

What is the term for the structure of a protein that has a native-like secondary structure content but without tightly packed protein interior?

Molten globule Signup and view all the answers

What is the main difference between the oxygen binding curves of myoglobin and hemoglobin?

Myoglobin has a hyperbolic curve, while hemoglobin has a sigmoidal curve Signup and view all the answers

What is the function of the R groups in the α-helix structure?

They project outward from the α-helix Signup and view all the answers

What is the main role of hydrophobic effect in protein folding?

To reduce entropy Signup and view all the answers

Why do globular proteins tend to have a higher proportion of polar side chains on the outside?

To interact with the aqueous environment Signup and view all the answers

What is the consequence of errors in protein folding?

Diseases such as Alzheimer's and Diabetes type 2 Signup and view all the answers

What is the location of hydrophobic residues in globular proteins?

Inside the protein Signup and view all the answers

What is the role of chaperones in protein folding?

To restore misfolded proteins Signup and view all the answers

What is the strategy used by chaperones to guide misfolded regions back into place?

A variety of strategies Signup and view all the answers

What refers to the linear amino acid sequence from the N-terminal end to the C-terminal end?

Primary structure Signup and view all the answers

What type of bonds are involved in the formation of α-helices?

Hydrogen bonds Signup and view all the answers

What is the characteristic of α-helices in terms of hydrogen bonding?

Hydrogen bonds are parallel to the axis Signup and view all the answers

Which bonds have free rotation in a protein?

Both A and B Signup and view all the answers

What is the term for local conformations maintained by extensive hydrogen bonding in a protein?

Secondary structure Signup and view all the answers

What type of structure involves extended, flat sheets?

β-sheet Signup and view all the answers

What is the consequence of errors in protein folding?

All of the above Signup and view all the answers

How many amino acids down the chain does the C=O of one amino acid hydrogen bond to in an α-helix?

4 Signup and view all the answers

What is the direction of the hydrogen bonds in an α-helix?

Parallel to the axis Signup and view all the answers

What is the secondary structure element that involves a regular pattern of hydrogen bonds between amide N-H and C=O groups?

All of the above Signup and view all the answers

What is the main reason for the decrease in hemoglobin's affinity for oxygen in the presence of BPG?

Changes in side chain electrostatics Signup and view all the answers

Which technique is used to study protein structure in solutions and membranes?

Multi-dimensional nuclear magnetic resonance Signup and view all the answers

What is the consequence of heat-induced denaturation of proteins?

Exposure of nonpolar segments to aqueous solvent Signup and view all the answers

What is the role of molecular chaperones in protein folding?

To ensure proper protein folding Signup and view all the answers

What is the cause of denaturation due to urea and guanidine?

Disruption of H-bonds Signup and view all the answers

What is the location of hydrophobic residues in membrane proteins?

In the membrane interior Signup and view all the answers

What is the effect of mercaptoethanol on protein structure?

Breakage of S-S bonds Signup and view all the answers

What is the result of errors in protein folding?

Decreased biological activity Signup and view all the answers

What is the main role of the hydrophobic effect in protein folding?

To reduce entropy in water Signup and view all the answers

What is the strategy used by chaperones to guide misfolded regions back into place?

Variety of strategies Signup and view all the answers

What is the primary reason for the disruption of an α-helix by proline?

The restricted rotation due to its cyclic structure Signup and view all the answers

What is the characteristic of the side chains in a globular protein?

They are predominantly polar and located outside the protein Signup and view all the answers

What is the effect of the proximity of several side chains of like charge on the α-helix structure?

It disrupts the α-helix due to electrostatic repulsion Signup and view all the answers

What is the characteristic of the polypeptide chain in a β-pleated sheet?

It lies adjacent to one another in a sheet-like structure Signup and view all the answers

What is the role of hydrogen bonding in the formation of an α-helix?

It forms a hydrogen bond between the N-H and C=O groups Signup and view all the answers

What is the primary function of hemoglobin in the blood?

To transport oxygen from the lungs to the tissues Signup and view all the answers

What is the effect of 2,3BPG on the oxygen binding behavior of hemoglobin?

It decreases the affinity of hemoglobin for oxygen Signup and view all the answers

What is the characteristic of the quaternary structure of hemoglobin?

It consists of multiple polypeptide chains Signup and view all the answers

What is the primary difference between the oxygen binding behavior of myoglobin and hemoglobin?

Hemoglobin exhibits cooperativity, while myoglobin does not Signup and view all the answers

What is the characteristic of fibrous proteins?

They are insoluble in water and have a fibrous structure Signup and view all the answers

What is maintained by extensive H-bonding that involves components of the peptide bond in a protein?

Secondary structure Signup and view all the answers

What is the direction of the H-bonds in an α-helix?

Parallel to the axis Signup and view all the answers

Which bonds in a protein have free rotation?

Bond between α-carbon and amino nitrogen, and bond between α-carbon and carboxyl carbon Signup and view all the answers

What type of structure is characterized by extended, flat sheets?

β-sheet Signup and view all the answers

What is the sequence of amino acids in a polypeptide chain referred to as?

Primary structure Signup and view all the answers

What is the characteristic of secondary structures in proteins?

Maintained by extensive H-bonding Signup and view all the answers

What is the direction of the hydrogen bonding in an α-helix?

From C=O of one amino acid to N-H of an amino acid that is four down the chain Signup and view all the answers

What type of protein structure involves local conformations maintained by extensive H-bonding?

Secondary structure Signup and view all the answers

Which of the following is a characteristic of α-helices in proteins?

Helical, coiled Signup and view all the answers

What is the role of hydrogen bonding in the formation of α-helices?

To maintain the helical structure Signup and view all the answers

What is the primary cause of denaturation due to pH changes?

Changes in side chain electrostatics Signup and view all the answers

What is the role of molecular chaperones in protein folding?

To restore misfolded proteins Signup and view all the answers

What is the effect of mercaptoethanol on protein structure?

Reduces S-S bonds Signup and view all the answers

What is the characteristic of the molten globule state?

Native-like secondary structure without a tightly packed protein interior Signup and view all the answers

What is the primary reason for the presence of hydrophobic residues inside globular proteins?

To reduce entropy in the presence of water Signup and view all the answers

What is the effect of heat on protein structure?

Causes disruptive vibrations Signup and view all the answers

What is the role of cryo-electron microscopy in protein structure determination?

To study protein structure using complex computational processing algorithms Signup and view all the answers

What is the primary cause of denaturation due to urea and guanidine?

Disruption of H-bonds Signup and view all the answers

What is the characteristic of protein denaturation?

The loss of structural order Signup and view all the answers

What is the strategy used by chaperones to guide misfolded regions back into place?

Using a variety of strategies to guide misfolded regions Signup and view all the answers

What is the approximate distance between each turn of an α-helix?

5.4 Å Signup and view all the answers

What is the main reason for the formation of a β-pleated sheet?

Hydrogen bonding between the backbone of sheets Signup and view all the answers

What is the characteristic of fibrous proteins?

They are insoluble in water and have a strong structure Signup and view all the answers

What is the term for the interaction between amino acid side chains in non-neighboring regions of the polypeptide chain?

Tertiary structure Signup and view all the answers

What is the function of hemoglobin in the lungs?

To bind oxygen and release CO2 and H+ Signup and view all the answers

What is the effect of BPG on hemoglobin's affinity for oxygen?

It decreases the affinity for oxygen Signup and view all the answers

What is the characteristic of the side chains in a globular protein?

Mostly polar on the outside and non-polar on the inside Signup and view all the answers

What is the term for the completely folded and compacted polypeptide chain?

Tertiary structure Signup and view all the answers

What is the role of proline in an α-helix?

It creates a bend in the α-helix Signup and view all the answers

What is the characteristic of the oxygen-binding curve of hemoglobin?

It is sigmoidal Signup and view all the answers

Study Notes

Protein Structure Fundamentals

1° structure of a protein refers to its linear amino acid sequence from the N-terminal to the C-terminal end.
Local conformations in proteins are maintained by extensive hydrogen bonding, particularly in secondary structures.
Free rotation occurs around the peptide bonds and the bonds involving the side chain, allowing flexibility.

α-Helices

α-Helices consist of hydrogen bonds between the amide N-H group of one amino acid and the C=O group of another, typically four residues away.
Each turn of an α-helix contains approximately 3.6 amino acids.
The hydrogen bonds in α-helices run parallel to the helix axis.
Proline introduces a bend in the α-helix because of its rigid structure and inability to adopt a helical conformation.
The presence of like-charged side chains nearby may destabilize the α-helix due to repulsion.

β-Pleated Sheets

β-Pleated sheets are characterized by extended, flat structures maintained by hydrogen bonding between strands.
In β-sheets, hydrogen bonds can connect distant parts of the polypeptide chain, contributing to stability.

Protein Classes

Globular proteins tend to have polar side chains on the exterior for interaction with the aqueous environment, while hydrophobic residues are tucked inside.
Fibrous proteins typically provide structural support and have elongated shapes.

Hemoglobin and BPG Interaction

Hemoglobin's primary function is gas transport, specifically oxygen delivery to tissues and CO2 transport from tissues back to the lungs.
2,3-BPG lowers hemoglobin's affinity for oxygen, facilitating oxygen release in tissues.
Hemoglobin also exhibits the Bohr effect, which describes the change in oxygen binding in response to pH and CO2 concentration shifts.

Protein Denaturation

Denaturation results from factors like heat, pH shifts, and chemical agents (urea, guanidine) that disrupt hydrogen bonding and protein structure.
Heat-induced denaturation leads to unfolding, loss of function, and potential aggregation.
Mercaptoethanol disrupts disulfide bonds, further altering protein conformation.

Role of Molecular Chaperones

Chaperones assist protein folding by preventing misfolding and aggregation, guiding misfolded regions back into proper conformation.
Chaperones can recognize and bind to exposed hydrophobic regions on nascent or misfolded proteins.

Structural Features and Techniques

Cryo-electron microscopy aids in protein structure determination by providing high-resolution images of proteins in their native states.
The molten globule state describes a partially folded state of proteins that retains some secondary structure but lacks a compact interior.

Summary of Key Characteristics

Secondary structures, including α-helices and β-sheets, rely on hydrogen bonds and specific amino acid interactions for stability.
The arrangement and characteristics of amino acid side chains contribute significantly to protein functionality and structure.
The overall structure of proteins influences their biological activity, interaction with other molecules, and response to environmental changes.

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Description

Test your knowledge of protein structure, including the primary sequence of amino acids and secondary structures like alpha helices and beta sheets.