Protein Secondary Structure and Stability

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Questions and Answers

What is the primary feature of amyloid structures in relation to normally soluble proteins?

They enhance the correct folding of proteins.

They convert to insoluble fibrils rich in β sheets. (correct)

They maintain their soluble state.

They replicate the activity of correctly folded proteins.

Which best describes the biochemical activities of the chemokine structure compared to the β-sheet structure?

They share similar receptor activation mechanisms.

Both bind to glycosaminoglycan simultaneously.

Both structures are equally stable.

They cannot perform their specific activities simultaneously. (correct)

What role does the heme group play in hemoglobin's function?

It aids in the breakdown of carbon dioxide.

It facilitates the binding and transport of oxygen. (correct)

It stabilizes the structure of hemoglobin.

It contributes to the iron metabolism of cells.

How does the stability of correctly folded proteins compare to their incorrectly folded counterparts based on the content?

They are marginally more stable. (B) Signup and view all the answers

What characterizes the structure of hemoglobin in terms of its subunits?

It is composed of two α and two β subunits. (B) Signup and view all the answers

What is the main function of hydrogen bonds in the alpha helix structure?

To stabilize the coiled structure of the polypeptide chain (C) Signup and view all the answers

Which statement accurately describes beta-sheets?

They are formed by fully extended polypeptide chains (C) Signup and view all the answers

What is the primary characteristic of reverse turns in polypeptide chains?

They create a 180° turn in the polypeptide chain (B) Signup and view all the answers

What role do disulfide bonds play in the stabilization of protein structures?

They contribute to the stability of extracellular proteins like antibodies (C) Signup and view all the answers

Which of the following best characterizes cysteine knots in proteins?

They consist of a specific arrangement of disulfide bonds (B) Signup and view all the answers

What effect do cysteine knots have on proteins?

They increase protein stability against denaturation and proteolysis (D) Signup and view all the answers

When discussing loops in polypeptide chains, their size can affect what aspect?

The proximity of amino acids within the loop (C) Signup and view all the answers

In beta-sheets, how are adjacent β-strands held together?

By hydrogen bonds formed between backbone CO and NH groups (A) Signup and view all the answers

What differentiates the α-helix from a β-strand in terms of structure?

The α-helix has R groups close to each other, β-strands do not (B) Signup and view all the answers

What characterizes inherently unstructured proteins (IUPs)?

They exist in multiple conformations until interacting with other molecules. (D) Signup and view all the answers

Which statement accurately describes metamorphic proteins?

They exist in an ensemble of structures of approximately equal energies. (C) Signup and view all the answers

What is an amyloid fibril?

A misfolded protein aggregate associated with diseases. (A) Signup and view all the answers

Which property is unique to lymphotactin?

It exhibits two very different structures that are in equilibrium. (D) Signup and view all the answers

How do alternative conformations of a peptide sequence influence protein folding?

They can facilitate or hinder the formation of the native structure. (D) Signup and view all the answers

What occurs to a protein during denaturation when exposed to 8 M urea and β-mercaptoethanol?

The protein becomes a randomly coiled polypeptide chain. (D) Signup and view all the answers

Which of these diseases is classified as an amyloidosis?

Alzheimer's disease (C) Signup and view all the answers

Why are disulfide bonds crucial in protein structure?

They stabilize the native structure of the protein. (A) Signup and view all the answers

What role do chemokines like lymphotactin play in the immune system?

They signal and bind to receptor proteins on immune-system cells. (C) Signup and view all the answers

What phenomenon describes the change in hemoglobin's structure upon ligand binding?

Conformational change (D) Signup and view all the answers

What best describes the profile of a folding funnel in protein folding thermodynamics?

It shows the relationship between entropy and stability during folding. (C) Signup and view all the answers

What does the concerted model of hemoglobin suggest about the T and R states?

Ligand binding shifts the equilibrium toward the R state. (B) Signup and view all the answers

What determines the conformation of a peptide?

Rotation about the single bonds in its backbone. (B) Signup and view all the answers

In the renaturation process, what role does β-mercaptoethanol play?

It promotes the emergence of disulfide bonds. (B) Signup and view all the answers

Which statement most accurately describes the behavior of hemoglobin as it binds oxygen?

Oxygen binding increases the likelihood of other oxygen molecules binding. (A) Signup and view all the answers

Which statement correctly describes the native conformation of a protein?

It is the most stable and enzymatically active form of the protein. (B) Signup and view all the answers

Which structure is primarily associated with risk factors for amyloidosis?

Beta sheets (C) Signup and view all the answers

Which of the following sequences is noted in the structural context of proteins?

The same sequence can exist in different types of secondary structures. (B) Signup and view all the answers

What is the primary significance of the 15-degree rotation of the αβ dimers in hemoglobin?

It indicates a conformational change associated with oxygen binding. (A) Signup and view all the answers

What function does β-mercaptoethanol serve in protein folding?

It removes urea and interacts with disulfide bonds. (B) Signup and view all the answers

What represents the state of a protein at the top of the folding funnel?

Randomly coiled polypeptide chains with maximum entropy. (B) Signup and view all the answers

Under which conditions does the T state of hemoglobin predominantly exist?

When no oxygen is bound (B) Signup and view all the answers

What is the result of removing urea while retaining a trace of β-mercaptoethanol during the renaturation process?

There is a slow regeneration of the protein's native structure. (A) Signup and view all the answers

What is the effect of oxygen binding on the affinity of hemoglobin for additional oxygen?

It enhances the likelihood of further oxygen binding. (B) Signup and view all the answers

What is the relationship between hemoglobin's R state and its oxygen affinity?

R state exhibits a higher affinity for oxygen than T state. (A) Signup and view all the answers

What occurs to the protein's enzymatic activity during the denaturation process?

Enzymatic activity is completely lost. (C) Signup and view all the answers

Study Notes

Secondary Structure

Alpha helix: a coiled structure stabilized by intrachain hydrogen bonds. The backbone CO and NH groups form hydrogen bonds, except at the helix ends. R groups project outward from the helix axis.
Beta sheets: formed by adjacent beta-strands. Polypeptide strands are fully extended, in contrast to the alpha helix. Three types of beta sheets exist: antiparallel, parallel and mixed.

Loops and Turns

Polypeptide chains can change direction via reverse turns and loops. Reverse turns are tight turns, where the polypeptide chain makes a 180° change in direction.

Disulfide Bridges

Covalent bonds formed between cysteine residues. Stabilize protein structures, particularly extracellular proteins like antibodies.

Cysteine Knots

Structural motifs in certain proteins. Characterized by a specific arrangement of disulfide bonds, creating a knotted topology within the protein's 3D structure. These knots provide exceptional stability preventing denaturation and proteolysis.

Tertiary Structure

Heptad repeats in coiled-coil proteins: Every seventh residue in each helix is leucine. The two helices are held together primarily by van der Waals interactions between the leucine residues.
Protein domains: independently folding regions within a polypeptide, connected by linkers. Examples include the four domains in the cell-surface protein CD4.

Quaternary Structure

Hemoglobin: a protein in red blood cells that binds/transports oxygen. It has a quaternary structure with four subunits (2 alpha and 2 beta). Each subunit contains a heme group which binds oxygen.
Hemoglobin's T state (deoxyhemoglobin) is low affinity for oxygen and, the R state (oxyhemoglobin) exhibits higher affinity for oxygen.
Hemoglobin's subunits interact in a cooperative manner. Binding of oxygen molecules causes conformational changes, increasing the affinity of other binding sites, facilitated by a sequential model
2,3-Bisphosphoglycerate: stabilizes the T state, facilitating oxygen release in tissues. Present in red blood cells.

Fetal Hemoglobin

Fetal hemoglobin binds oxygen at lower pO2 than adult hemoglobin thus facilitating the transfer of oxygen from maternal Hb to fetal Hb. Fetal hemoglobin differs from adult hemoglobin by substituting the beta chain with a gamma chain, reducing its affinity for 2,3-BPG. This higher oxygen affinity allows fetal hemoglobin to acquire oxygen more easily from maternal hemoglobin.

Mutations

Mutations in hemoglobin genes can cause diseases, such as sickle cell anemia. This disease arises due to a mutation, substituting glutamic acid with valine in the beta chain. These substitutions create hydrophobic patches which promote the aggregation of hemoglobin, leading to the formation of insoluble fibers. These aggregates change the shape of red blood cells, making them rigid and sickle-shaped, compromising their oxygen-carrying capacity.

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Description

This quiz explores key concepts related to the secondary structure of proteins, including alpha helices, beta sheets, and the role of disulfide bridges. Understand how loops and cysteine knots contribute to the overall stability of protein structures. Test your knowledge of these essential biochemical motifs.