Biochem 2.3 Protein Folding and Stability

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Questions and Answers

What is the main purpose of protein folding?

To achieve the highest possible energy state

To increase the number of states available to the protein

To minimize protein interactions

To adopt a functional secondary and tertiary structure (correct)

Which phenomenon drives the majority of protein folding?

Electrostatic interactions

The hydrophobic effect (correct)

Van der Waals forces

Covalent bonding

What occurs to the entropy of a protein when it folds?

It remains unchanged

It fluctuates unpredictably

It increases significantly

It decreases (correct)

What happens to the entropy of the surrounding water when proteins fold?

It increases significantly Signup and view all the answers

Why is the exposure of hydrophobic residues to water energetically unfavorable?

Water can only interact with hydrophilic groups Signup and view all the answers

What is formed around molecules dissolved in water?

A solvation shell Signup and view all the answers

Which interactions are more favorable between water and protein groups?

Hydrophilic interactions Signup and view all the answers

What does conformational stability of a protein primarily depend on?

The free energy change between folded and unfolded forms Signup and view all the answers

Which factor indicates that a protein is more stable in its folded form?

Higher melting temperature than other proteins Signup and view all the answers

What is indicated by a high concentration of denaturing agent required to denature a protein?

The protein is more stable Signup and view all the answers

What usually happens to proteins that become trapped in stable intermediate conformations?

They can become nonfunctional Signup and view all the answers

What is the significance of the melting temperature in protein studies?

It represents the temperature at which a protein is fully denatured Signup and view all the answers

What effect does high pH have on lysine residues in proteins?

It leads to the deprotonation of lysine. Signup and view all the answers

How do changes in salt concentration affect the structure of proteins?

They disrupt interactions between charged surface residues. Signup and view all the answers

What is the role of the hydrophobic effect in protein tertiary structure?

It largely determines the shape by promoting hydrophobic interactions. Signup and view all the answers

What happens to the hydrophobic core of a protein under extreme pH changes?

It remains mostly intact regardless of the pH level. Signup and view all the answers

How do denaturing agents like sodium dodecyl sulfate (SDS) affect proteins?

They interact with the hydrophobic residues, disrupting the hydrophobic core. Signup and view all the answers

Which of the following statements regarding pH and protein shape is accurate?

Extreme pH levels can alter the protein's nonfunctional shape. Signup and view all the answers

What effect do positively charged ions have on interactions within proteins?

They can outcompete positively charged residues for anionic interactions. Signup and view all the answers

What role does the pH play in the interaction between lysine and glutamate?

It affects the protonation state that can alter their interaction. Signup and view all the answers

What is generally affected by changes in salt concentration in proteins?

Interactions between charged surface residues. Signup and view all the answers

What can cause a protein to adopt a new shape?

Changes in salt concentration, pH, and temperature Signup and view all the answers

What is the term used for the process when a protein loses its structure due to environmental changes?

Denaturation Signup and view all the answers

Which of the following factors is NOT mentioned as affecting a protein's conformation?

Oxygen concentration Signup and view all the answers

How does an increase in temperature generally affect proteins?

It can increase the kinetic energy of amino acid residues. Signup and view all the answers

What happens to the energy landscape of a protein during denaturation?

It becomes less favorable for folding. Signup and view all the answers

Which condition can directly lead to the unfolding of a protein?

A decrease in pH Signup and view all the answers

Which of the following statements is true regarding the stability of proteins?

Some proteins can withstand extreme conditions without losing function. Signup and view all the answers

What role do ligands play in protein conformation?

They can induce changes in the protein's shape. Signup and view all the answers

What is a consequence of a protein undergoing spontaneous denaturation?

It may lose much or all of its functional structure. Signup and view all the answers

Which of the following describes a potential effect of chemical alterations to a protein?

Alters the primary structure and may affect conformation. Signup and view all the answers

What occurs first during the formation of protein secondary structures?

Local secondary structures are formed. Signup and view all the answers

How are the energetics of protein folding often represented?

As a funnel. Signup and view all the answers

What is a characteristic of proteins in regards to their conformational states?

They undergo constant movement and changes. Signup and view all the answers

What happens when a protein adopts a brief higher-energy conformation?

It quickly returns to a low-energy conformation. Signup and view all the answers

What limits the conformational changes a protein can explore?

Certain conformations requiring too much energy input. Signup and view all the answers

When a protein's local environment changes, what can happen to its energy landscape?

It may allow a higher-energy conformation to stabilize. Signup and view all the answers

What is indicated by the process of funneling in protein folding?

Proteins tend to move toward the lowest-energy conformation possible. Signup and view all the answers

What typically characterizes the highly structured regions of a protein?

They tend to remain near the lowest-energy conformation. Signup and view all the answers

What effect does maintaining constant conditions have on proteins?

It enables quick return to low-energy conformations. Signup and view all the answers

Study Notes

Protein Folding and Stability

Protein folding is the process by which proteins adopt their functional secondary and tertiary structures.
Proteins fold to achieve the lowest possible energy state by maximizing favorable interactions, minimizing unfavorable interactions, and maximizing the total of the system.
Protein folding is spontaneous under physiological conditions.

The Hydrophobic Effect

The hydrophobic effect is the dominant driving force in most protein folding.
Burying hydrophobic residues inside the protein is energetically favorable.
This involves a decrease in the protein's entropy, but this is offset by a much larger increase in water's entropy.
Unfolded proteins expose hydrophobic residues to water, which forms highly ordered water molecules around them.
When the protein folds, burying hydrophobic residues, water molecules become less ordered increasing the system's entropy.
Interactions between water and hydrophilic groups are highly favorable.

Peptides and Proteins

Hydrophobic residues interact with each other through London dispersion forces, contributing to the stability of the protein.
Hydrophilic residues also contribute to stability via interactions with each other and water.
Protein folding involves a sequence of steps starting with local secondary structures.
Interactions between these secondary structures lead to protein folding into its final tertiary structure.
Multiple factors contribute to protein folding, including hydrophobic interactions and hydrogen bonding.
The protein folding process is highly dynamic, with constant conformational changes taking place.

Denaturation

Proteins can be denatured by changes in temperature, pH, salt concentration, or chemical denaturing agents.
Denaturation disrupts the protein's structure, leading to a loss of its biological function.
Denaturing agents disrupt the hydrophobic effect and other intermolecular forces that stabilize protein structure.
Some proteins can refold after denaturing conditions are removed, while others may not be able to do so.

Protein Conformational Stability

Conformational stability describes the protein's tendency to remain in its folded state.
The folding process of proteins is often modeled as a funnel, where the narrow neck represents the stable native conformation.
A measure of protein folding is the melting temperature, which is the temperature at which half of the proteins in solution become unfolded.

Protein Misfolding

Misfolding occurs when proteins adopt non-native conformations, leading to their inability to function properly.
Misfolded proteins can aggregate, forming harmful structures.
Chaperones (heat shock proteins) provide a protective environment within cells allowing proteins to properly fold and to prevent aggregation.

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Description

Explore the intricate processes of protein folding and the hydrophobic effect with this quiz. Understand how proteins achieve their functional structures and the energetic principles driving these transformations. Test your knowledge on key concepts like stability, entropy, and interactions in protein folding.